1H NMR-based metabolomic study of metabolic profiling for the urine of kidney stone patients

The Plasma Metabolome and Risk of Incident Kidney Stones

Key Points

Background

Information on metabolomic profiles in kidney stone formers is limited. To examine independent associations between plasma metabolomic profiles and the risk of incident, symptomatic kidney stones in adults, we conducted prospective nested case-control studies in two large cohorts.

Methods

We performed plasma metabolomics on 1758 participants, including 879 stone formers (346 from the Health Professionals Follow-Up Study [HPFS] cohort, 533 from the Nurses' Health Study [NHS] II cohort) and 879 non–stone formers (346 from HPFS, 533 from NHS II) matched for age, race, time of blood collection, fasting status, and (for NHS II) menopausal status and luteal day of menstrual cycle for premenopausal participants. Conditional logistic regression models were used to estimate the odds ratio (OR) of kidney stones adjusted for body mass index; hypertension; diabetes; thiazide use; and intake of potassium, animal protein, oxalate, dietary and supplemental calcium, caffeine, and alcohol. A plasma metabolite–based score was developed in each cohort in a conditional logistic regression model with a lasso penalty. The scores derived in the HPFS (“kidney stones metabolite score [KMS]_HPFS”) and the NHS II (“KMS_NHS”) were tested for their association with kidney stone risk in the other cohort.

Results

A variety of individual metabolites were associated with incident kidney stone formation at prespecified levels of metabolome-wide statistical significance. We identified three metabolites associated with kidney stones in both HPFS and NHS II cohorts: β-cryptoxanthin, sphingomyelin (d18:2/24:1, d18:1/24:2), and sphingomyelin (d18:2/24:2). The standardized KMS_HPFS yielded an OR of 1.23 (95% confidence interval, 1.05 to 1.44) for stones in the NHS II cohort. The standardized KMS_NHS was in the expected direction but did not reach statistical significance in HPFS (OR, 1.16; 95% confidence interval, 0.97 to 1.39).

Conclusions

The findings of specific metabolites associated with kidney stone status in two cohorts and a plasma metabolomic signature offer a novel approach to characterize stone formers.

The urinary microbiota composition and functionality of calcium oxalate stone formers

Background

Accumulated evidences indicate that dysbiosis of the urinary microbiota is associated with kidney stone formation. In the present study, we aimed to investigate the urinary microbiota composition and functionality of patients with calcium oxalate stones and compare it with those of healthy individuals.

Method

We collected bladder urine samples from 68 adult patients with calcium oxalate stones and 54 age-matched healthy controls by transurethral catheterization. 16S rRNA gene and shotgun sequencing were utilized to characterize the urinary microbiota and functionality associated with calcium oxalate stones.

Results

After further exclusion, a total of 100 subjects was finally included and analyzed. The diversity of the urinary microbiota in calcium oxalate stone patients was not significantly different from that of healthy controls. However, the urinary microbiota structure of calcium oxalate stone formers significantly differed from that of healthy controls (PERMANOVA, r = 0.026, P = 0.019). Differential representation of bacteria (e.g., Bifidobacterium) and several enriched functional pathways (e.g., threonine biosynthesis) were identified in the urine of calcium oxalate stone patients.

Conclusion

Our results showed significantly different urinary microbiota structure and several enriched functional pathways in calcium oxalate stone patients, which provide new insight into the pathogenesis of calcium oxalate stones.

Metabolomic profiles and pathogenesis of nephrolithiasis

PURPOSE OF REVIEW

Kidney stone disease is caused by supersaturation of urine with certain metabolites and minerals. The urine composition of stone formers has been measured to prevent stone recurrence, specifically calcium, uric acid, oxalate, ammonia, citrate. However, these minerals and metabolites have proven to be unreliable in predicting stone recurrence. Metabolomics using high throughput technologies in well defined patient cohorts can identify metabolites that may provide insight into the pathogenesis of stones as well as offer possibilities in therapeutics.

RECENT FINDINGS

Techniques including 1H-NMR, and liquid chromatography paired with tandem mass spectroscopy have identified multiple possible metabolites involved in stone formation. Compared to formers of calcium oxalate stones, healthy controls had higher levels of hippuric acid as well as metabolites involved in caffeine metabolism. Both the gut and urine microbiome may contribute to the altered metabolome of stone formers.

SUMMARY

Although metabolomics has offered several potential metabolites that may be protective against or promote stone formation, the mechanisms behind these metabolomic profiles and their clinical significance requires further investigation.

Untargeted and targeted metabolomics reveal bile acid profile changes in rats with ethylene glycol-induced calcium oxalate nephrolithiasis

Calcium oxalate (CaOx) nephrolithiasis is a prevalent disorder linked to metabolism. Examining metabolic alterations could potentially give an initial understanding of the origins of CaOx nephrolithiasis. This study aims to determine gut metabolic biomarkers differentiating CaOx nephrolithiasis utilizing untargeted and targeted metabolomics. CaOx nephrolithiasis model rats were built by 1% ethylene glycol administration. Histologic staining and renal function measurement revealed the presence of crystals in the lumen of the renal tubules, the renal injury and interstitial fibrosis in CaOx rats, demonstrating that the models of CaOx were established successfully. Hematoxylin & eosin (H&E) staining showed that CaOx group had inflammation and damage in the ileal tissue. Immunofluorescence and PCR results displayed that the tight junction proteins, ZO-1 and Occludin levels were decreased in the ileal tissues of the CaOx group. The untargeted metabolomic analysis revealed that 269 gut metabolites were differentially expressed between the CaOx group and the control group. Meanwhile, bile secretion, the main metabolic pathway in CaOx nephrolithiasis, was identified. Following, five significant bile acid metabolites were selected utilizing the targeted bile acid metabolomics, including Hyodeoxycholic acid (HDCA), Glycohyodeoxycholic acid (GHDCA), Nor-Deoxycholic Acid, omega-muricholic acid, and Taurolithocholic acid. Among these metabolites, HDCA and GHDCA presented the highest predictive accuracy with AUC = 1 to distinguish the CaOx group from the control group. As a result of network pharmacology, target genes of HDCA and GHDCA in CaOx nephrolithiasis were enriched in oxidative stress and apoptosis pathways. Conclusively, our study provides insight into bile acids metabolic changes related to CaOx nephrolithiasis. Although alterations in biochemical pathways indicate a complex pathology in CaOx rats, bile acid changes may serve as biomarkers of CaOx nephrolithiasis.

Application of metabolomics in urolithiasis: the discovery and usage of succinate

Urinary stone is conceptualized as a chronic metabolic disorder punctuated by symptomatic stone events. It has been shown that the occurrence of calcium oxalate monohydrate (COM) during stone formation is regulated by crystal growth modifiers. Although crystallization inhibitors have been recognized as a therapeutic modality for decades, limited progress has been made in the discovery of effective modifiers to intervene with stone disease. In this study, we have used metabolomics technologies, a powerful approach to identify biomarkers by screening the urine components of the dynamic progression in a bladder stone model. By in-depth mining and analysis of metabolomics data, we have screened five differential metabolites. Through density functional theory studies and bulk crystallization, we found that three of them (salicyluric, gentisic acid and succinate) could effectively inhibit nucleation in vitro. We thereby assessed the impact of the inhibitors with an EG-induced rat model for kidney stones. Notably, succinate, a key player in the tricarboxylic acid cycle, could decrease kidney calcium deposition and injury in the model. Transcriptomic analysis further showed that the protective effect of succinate was mainly through anti-inflammation, inhibition of cell adhesion and osteogenic differentiation. These findings indicated that succinate may provide a new therapeutic option for urinary stones.

Mechanisms of the intestinal and urinary microbiome in kidney stone disease

Kidney stone disease affects ~10% of the global population and the incidence continues to rise owing to the associated global increase in the incidence of medical conditions associated with kidney stone disease including, for example, those comprising the metabolic syndrome. Considering that the intestinal microbiome has a substantial influence on host metabolism, that evidence has suggested that the intestinal microbiome might have a role in maintaining oxalate homeostasis and kidney stone disease is unsurprising. In addition, the discovery that urine is not sterile but, like other sites of the human body, harbours commensal bacterial species that collectively form a urinary microbiome, is an additional factor that might influence the induction of crystal formation and stone growth directly in the kidney. Collectively, the microbiomes of the host could influence kidney stone disease at multiple levels, including intestinal oxalate absorption and direct crystal formation in the kidneys.

1H NMR metabolic profiling of Staphylococcus pseudintermedius isolated from canine uroliths

Staphylococcus pseudintermedius is a urease-producing bacteria which is a major cause of magnesium ammonium phosphate (MAP) urolithiasis in canine. A positive urolith culture is an important risk factor for MAP urolithiasis in canine. The mechanism underlying the metabolic changes of S. pseudintermedius after crystallization in artificial urine (AU) needs more defined baseline metabolic information. Therefore, we extensively investigated the metabolic changes of S. pseudintermedius extensively after crystallization in AU. A high urease activity and positive biofilm formation strain, entitled the S. pseudintermedius (SPMAP09) strain, was isolated from canine MAP uroliths, and analyzed using nuclear magnetic resonance (NMR) spectroscopy-based metabolomics. The molecular mechanism-specific metabolic phenotypes were clearly observed after crystallization in AU at day 3. The crystals induced by SPMAP09 were also confirmed and the major chemical composition identified as struvite. Interestingly, our findings demonstrated that a total of 11 identified metabolites were significantly changed. The levels of formate, homocarnosine, tyrosine, cis-aconitate, glycolate, ethyl malonate, valine and acetate level were significantly higher, accompanied with decreased levels of inosine, glucose, and threonine at day 3 compared with the initial time-point (day 0). In addition, our results exhibited that the glyoxylate and dicarboxylate metabolism was significantly related to the SPMAP09 strain at day 3 in AU. Thus, metabolic changes of the SPMAP09 strain after crystallization in AU potentially helps to explain the preliminary molecular mechanism for the crystals induced by S. pseudintermedius.

Nuclear Magnetic Resonance Metabolomic Profiling and Urine Chemistries in Incident Kidney Stone Formers Compared with Controls

BACKGROUND

The urine metabolites and chemistries that contribute to kidney stone formation are not fully understood. This study examined differences between the urine metabolic and chemistries profiles of first-time stone formers and controls.

METHODS

High-resolution 1H-nuclear magnetic resonance (NMR) spectroscopy-based metabolomic analysis was performed in 24-hour urine samples from a prospective cohort of 418 first-time symptomatic kidney stone formers and 440 controls. In total, 48 NMR-quantified metabolites in addition to 12 standard urine chemistries were assayed. Analysis of covariance was used to determine the association of stone former status with urine metabolites or chemistries after adjusting for age and sex and correcting for the false discovery rate. Gradient-boosted machine methods with nested cross-validation were applied to predict stone former status.

RESULTS

Among the standard urine chemistries, stone formers had lower urine oxalate and potassium and higher urine calcium, phosphate, and creatinine. Among NMR urine metabolites, stone formers had lower hippuric acid, trigonelline, 2-furoylglycine, imidazole, and citrate and higher creatine and alanine. A cross-validated model using urine chemistries, age, and sex yielded a mean AUC of 0.76 (95% CI, 0.73 to 0.79). A cross-validated model using urine chemistries, NMR-quantified metabolites, age, and sex did not meaningfully improve the discrimination (mean AUC, 0.78; 95% CI, 0.75 to 0.81). In this combined model, among the top ten discriminating features, four were urine chemistries and six NMR-quantified metabolites.

CONCLUSIONS

Although NMR-quantified metabolites did not improve discrimination, several urine metabolic profiles were identified that may improve understanding of kidney stone pathogenesis.

Urinary Microbial and Metabolomic Profiles in Kidney Stone Disease

Background

Kidney stones or nephrolithiasis is a chronic metabolic disease characterized by renal colic and hematuria. Currently, a pathogenetic mechanism resulting in kidney stone formation remains elusive. We performed a multi-omic study investigating urinary microbial compositions and metabolic alterations during nephrolithiasis.

Method

Urine samples from healthy and individuals with nephrolithiasis were collected for 16S rRNA gene sequencing and liquid chromatography-mass spectroscopy. Microbiome and metabolome profiles were analyzed individually and combined to construct interactome networks by bioinformatic analysis.

Results

Distinct urinary microbiome profiles were determined in nephrolithiasis patients compared with controls. Thirty-nine differentially abundant taxa between controls and nephrolithiasis patients were identified, and Streptococcus showed the most significant enrichment in nephrolithiasis patients. We also observed significantly different microbial compositions between female and male nephrolithiasis patients. The metabolomic analysis identified 112 metabolites that were differentially expressed. Two significantly enriched metabolic pathways, including biosynthesis of unsaturated fatty acids and tryptophan metabolism, were also identified in nephrolithiasis patients. Four potentially diagnostic metabolites were also identified, including trans-3-hydroxycotinine, pyroglutamic acid, O-desmethylnaproxen, and FAHFA (16:0/18:2), and could function as biomarkers for the early diagnosis of nephrolithiasis. We also identified three metabolites that contributed to kidney stone size. Finally, our integrative analysis of the urinary tract microbiome and metabolome identified distinctly different network characteristics between the two groups.

Conclusions

Our study has characterized important profiles and correlations among urinary tract microbiomes and metabolomes in nephrolithiasis patients for the first time. These results shed new light on the pathogenesis of nephrolithiasis and could provide early clinical biomarkers for diagnosing the disease.

Delineating the role of the urinary metabolome in the lithogenesis of calcium-based kidney stones

OBJECTIVE

To delineate the role of the urinary metabolome in the genesis of urinary stone disease (USD).

METHODS

Untargeted metabolomics was utilized in comparative analyses of calcium-based stones (CBS) and spot urine samples from patients with a history of USD with or without urinary stone activity based on radiologic imaging. Stone and urine metabolomes were stratified by composition and radiographic stone-activity, respectively. Additionally, we quantified highly abundant metabolites that were present in either calcium oxalate (CaOx) or calcium phosphate (CaPhos) stones and also significantly enriched in the urine of active stone formers (SF) compared to non-active SF. These data were used to delineate either a direct involvement of urinary metabolites in lithogenesis or the passive uptake of biomolecules within the stone matrix.

RESULTS

Urinary metabolomes were distinct based on radiographic stone-activity and the two types of CBS. Stratification by radiologic stone activity was driven by the enrichment of 14 metabolites in the urine of active SF that were also highly abundant in both CaOx and CaPhos stones, indicative of a potential involvement of these metabolites in lithogenesis. Using the combination of these 14 metabolites in total, we generated a model that correctly classified patients as either active vs non-active SF in a prospectively recruited cohort with 73% success.

CONCLUSIONS

Collectively, our data suggest specific urinary metabolites directly contribute to the formation of urinary stones and that active SF may excrete higher levels of lithogenic metabolites than non-active patients. Future studies are needed to confirm these findings and establish the causative mechanisms associated with these metabolites.

Why is diagnosis, investigation and improved management of kidney stone disease important? Non-pharmacological and pharmacological treatments for nephrolithiasis

INTRODUCTION

Progress in the medical treatment and management of nephrolithiasis has been limited to date and continues to depend on urinary metabolic screening to assess excretion of the main stone constituents, factors determining stone solubility and precipitation, and on dietary and lifestyle recommendations.

AREAS COVERED

In this review, we try to highlight some of the broader aspects of kidney stone disease in relation to recent epidemiological and pathophysiological findings, and emerging new treatments. Specifically, this review will cover recent evidence on the association between metabolic risk factors and kidney stone disease, dietary risk factors and dietary interventions to prevent kidney stones, and how genomics, metabolomics and proteomics may improve diagnosis and treatment of this troublesome, if rarely fatal, condition. PubMed was used to identify the most suitable references according to our search strategy; only full manuscripts were included.

EXPERT OPINION

What is emerging is that kidney stone disease is not an isolated disorder, but is systemic in nature with links to important and common co-morbidities such as diabetes, hypertension, cardiovascular disease, and chronic kidney disease. These associations support the need to take nephrolithiasis seriously as a medical condition and to adopt a more holistic approach to its investigation and treatment.

Methods for the dietary assessment of adult kidney stone formers: a scoping review

BACKGROUND

Kidney stones are a frequent and potentially severe condition, affecting 5-10% of the European population. Causes are multifactorial, diet in particular plays a major role in the formation and management of kidney stones. The aim of this scoping review is to assess the methods used to study the diet of adult kidney stone formers.

METHODS

We conducted a systematic search in Medline Ovid SP, Embase, Cinahl, Cochrane (CENTRAL), Web of Sciences databases on June 10th, 2020. Self-report methods (such as food frequency questionnaires or 24-h dietary recalls), objective nutritional biomarkers and controlled diets were considered. We analyzed the selected publications based on the origin of participants, study design and dietary assessment methods used.

RESULTS

We screened 871 publications and included 162 of them. Most studies included participants from North America and Europe and were observational. Short and cost-effective tools such as food frequency questionnaires and other questionnaires were the most frequently used. Moreover, food diary was a frequently selected method to study the diet of kidney stone formers. New technologies (e.g. online questionnaires, phone applications, connected tools) were rarely used.

CONCLUSION

Accurate reporting of the methods used in nutritional studies is of key importance to interpret results and build evidence. Assessing long-term dietary intake is still a challenge for nutritional epidemiology. A combination of self-report methods with objective dietary biomarkers and new technologies probably represents the best way forward.

Omics in urology: An overview on concepts, current status and future perspectives

Recent technological advances in molecular biology have led to great progress in the knowledge of structure and function of cells and their main constituents. In this setting, 'omics' is standing out in order to significantly improve the understanding of etiopathogenetic mechanisms of disease and contribute to the development of new biochemical diagnostics and therapeutic tools. 'Omics' indicates the scientific branches investigating every aspect of cell's biology, including structures, functions and dynamics pathways. The main 'omics' are genomics, epigenomics, proteomics, transcriptomics, metabolomics and radiomics. Their diffusion, success and proliferation, addressed to many research fields, has led to many important acquisitions, even in Urology. Aim of this narrative review is to define the state of art of 'omics' application in Urology, describing the most recent and relevant findings, in both oncological and non-oncological diseases, focusing the attention on urinary tract infectious, interstitial cystitis, urolithiasis, prostate cancer, bladder cancer and renal cell carcinoma. In Urology the majority of 'omics' applications regard the pathogenesis and diagnosis of the investigated diseases. In future, its role should be implemented in order to develop specific predictors and tailored treatments.

Metabolomics analysis of the serum from children with urolithiasis using UPLC-MS

Pediatric urolithiasis is a common urologic disease with high morbidity and recurrence rates. Recent studies have shown that metabolic dysfunction plays a vital role in the pathogenesis of urolithiasis, especially in children, but the specific mechanism is still unclear. Metabolomics is an ideal technology for exploring the mechanism of metabolic disorders in urolithiasis. In the present study, a serum metabolomics based on ultra‐performance liquid chromatography mass spectrometry was performed. A total of 50 children subjects were recruited for the study, including 30 patients with kidney stones and 20 normal controls (NCs). Principal component analysis and orthogonal partial least‐squares determinant analysis were carried, and 40 metabolites were found to be significantly altered in patients with kidney stones, mainly involving retinol metabolism, steroid hormone biosynthesis, and porphyrin and chlorophyll metabolism. The kidney stone group appeared to have a lower serum level of bilirubin, but a relative higher level of retinal, all‐transretinoic acid, progesterone, and prostaglandin E2 compared with those of the NC group. All the findings suggest that patients with urolithiasis have several metabolic characteristics, which are related to stone formation or compensation. These metabolites and pathways are very likely associated with development of kidney stones and should be considered as potential novel targets for treatment and prevention.

Advantages of Herbal Over Allopathic Medicine in the Management of Kidney and Urinary Stones Disease

Kidney and urinary stone disease (Nephrolithiasis and urolithiasis) are the condition where urinary stones or calculi are formed in the urinary tract. The problem of urinary stones is very ancient; these stones are found in all parts of the urinary tract, kidney, ureters, and the urinary bladder and may vary considerably in size. It is a common disease estimated to occur in approximately 12% of the population, with a recurrence rate of 70-81% in males and 47-60% in females. The treatment of kidney and urinary stone diseases such as a western (allopathy) medicine and surgery is now in trends. However, most people preferred plant-based (herbal) therapy because of the overuse of allopathic drugs, which results in a higher incidence rate of adverse or severe side effects. Therefore, people every year turn to herbal therapy because they believe plant-based medicine is free from undesirable side effects, although herbal medicines are generally considered to be safe and effective. In the present article, an attempt has been made to emphasize an herbal therapy is better than allopathic therapy for the management of the kidney and urinary stone disease.

A Specific Urinary Amino Acid Profile Characterizes People with Kidney Stones

Background

Urolithiasis is the process of stone formation in the urinary tract. Its etiology is only partly known, and efficient therapeutic approaches are currently lacking. Metabolomics is increasingly used in biomarkers discovery for its ability to identify mediators of relevant (patho)physiological processes. Amino acids may be involved in kidney stone formation. The aim of the present study was to investigate the presence of an amino acid signature in stone former urine through a targeted metabolomic approach.

Methods

A panel of 35 amino acids and derivatives was assessed in urines from 15 stone former patients and 12 healthy subjects by UPLC-MS. Partial Least Squares Discriminant Analysis (PLS-DA) was used to define amino acid profiles of cases and controls. Results and Discussion. Our approach led to the definition of a specific amino acid fingerprint in people with kidney stones. A urinary amino acid profile of stone formers was characterized by lower levels of α-aminobutyric acid, asparagine, ethanolamine, isoleucine, methionine, phenylalanine, serine, tryptophan, and valine. Metabolomic analysis may lend insights into the pathophysiology of urolithiasis and allow tracking this prevalent condition over time.