A Specific Urinary Amino Acid Profile Characterizes People with Kidney Stones

Metabolomics study by metabolite profiling analysis in kidney and liver of calorie-restricted aging rats using GC-MS/MS

Aging leads to deterioration of the liver and kidney. Metabolic research on aging organs, including liver and kidney and metabolic studies of caloric restriction (CR), which delay aging and extends lifespan, are not well understood. In this study, we monitored metabolic changes associated with aging and explored potential biomarkers in kidney and liver of young (Y, 8 months), old (O, 23 months), and old calorie-restricted (OCR, 23 months) rats by metabolic profiling of organic acids (OA), free fatty acids (FFA), amino acids (AA) using gas chromatography-tandem mass spectrometry. Optimization of OA, FFA, and AA profiling methods were useful for quantifying these metabolites in kidney and liver. Profile analysis identified 48 and 45 metabolites in the kidney and liver, respectively. In the kidney, malic acid was significantly higher when comparing the Y and O groups, whereas 3-hydroxybutyric acid was significantly higher when comparing the O and OCR groups. In the liver, four metabolites (phenylacetic acid, valine, isoleucine, and tyrosine) were significantly evaluated as potential biomarker when comparing the Y and O groups, whereas 3-hydroxybutyric acid was significantly increased when comparing the O and OCR groups. Metabolomics results indicate that aging leads to mitochondrial dysfunction, phenylalanine metabolism disorders, and kidney dysfunction, whereas CR may regulate renal aging by reducing oxidative stress, inflammation, and lipid accumulation, while improving energy metabolism and resistance to oxidative stress in the liver. This result may explain some changes in the metabolism of aged kidney and liver during aging and CR.

2bRAD-M Reveals the Characteristics of Urinary Microbiota in Overweight Patients with Urinary Tract Stones

Background: Urinary tract stone (UTS) is a common disease significantly impacting human health. Obesity influences stone formation and increases UTS incidence, yet the differences in the urinary microbiota and pathways between overweight and healthy-weight UTS patients remain unclear. Methods: In this study, 16 patients were analyzed: 8 overweight and 8 healthy-weight UTS patients. Bladder urine samples were collected during surgery, and DNA was extracted for microbial analysis using 2bRAD markers. Microbial diversity and KEGG pathway differences were studied. Results: The results showed that overweight UTS patients had a significantly higher urinary microbial diversity than healthy-weight patients. The analysis identified differences in microbiota at various taxonomic levels. LEfSe analysis revealed Sphingomonas_paucimobilis as abundant in overweight patients, while Bifidobacterium_piotii dominated in healthy-weight patients. Key species, including Ralstonia_sp000620465, Sphingomonas_paucimobilis, and Campylobacter_D_coli, were identified. KEGG analysis highlighted enriched pathways in overweight UTS patients, including the porphyrin and chlorophyll metabolism, fatty acid metabolism, amino acid degradation, and renin-angiotensin and mineral absorption pathways. Conclusions: This study is the first to use 2bRAD-M microbiome analysis to compare the urinary microbiota between overweight and healthy-weight UTS patients. It identified significant microbiota and pathway differences, suggesting a link between microbiota imbalance, obesity, and stone formation. These findings provide potential targets for further research on obesity-related stone susceptibility mechanisms.

Mitochondrial enzyme HIBADH protects against calcium oxalate nephrolithiasis by modulating oxidative stress and apoptosis

Calcium oxalate (CaOx) nephrolithiasis, as one of the most common types of kidney stones, poses a major threat to human health. This study aimed to investigate the role of 3-hydroxyisobutyrate dehydrogenase (HIBADH) in the pathogenesis of CaOx nephrolithiasis. CaOx nephrolithiasis models were established in rats via 1 % ethylene glycol and 2 % ammonium chloride induction and in HK-2 cells using calcium oxalate monohydrate (COM, 100 μg/mL). HIBADH expression was modulated through plasmid transfection and siRNA knockdown in vitro, and AAV2/9-mediated gene transfer in vivo. Multiple parameters were assessed, including cell crystal adhesion, apoptosis, cell cycle distribution, oxidative stress markers (SOD, MDA, MitoSOX fluorescence), and mitochondrial function (ATP level, mitochondrial membrane potential), using various techniques such as crystal adhesion assay, flow cytometry, western blot, qRT-PCR, and fluorescence microscopy. Kidney tissues were analyzed through H&E, Von Kossa, and PAS staining. Results demonstrated that HIBADH expression was significantly downregulated in CaOx nephrolithiasis rats and COM-treated HK-2 cells. In vitro, HIBADH overexpression reduced cell crystal adhesion and apoptosis, promoted cell cycle progression, mitigated mitochondria-involved cellular oxidative stress, and enhanced mitochondrial function in COM-induced HK-2 cells. In vivo, AAV2/9-mediated HIBADH overexpression attenuated crystal deposits and tubular injury, reduced apoptosis, and mitigated mitochondria-involved cellular oxidative stress in kidney tissues. The mitochondria-targeted antioxidant Mito-TEMPO counteracted the effects of HIBADH silencing, highlighting the role of mitochondrial function in HIBADH's protective mechanism. This study identifies HIBADH as a critical regulator in CaOx nephrolithiasis, exerting its protective effects through modulation of mitochondrial function and mitochondria-involved cellular oxidative stress, cell crystal adhesion, and apoptosis. Our findings elucidate the link between mitochondrial metabolism and kidney stone formation, positioning HIBADH as a key protective factor and a promising candidate with therapeutic potential for CaOx nephrolithiasis.

A New Perspective on Gas Chromatography-Mass Spectrometry Urinary Metabolomic Analysis and Efficient Risk Assessment of Urolithiasis: Morning Urine Organic Acid Profiles

INTRODUCTION

Urolithiasis is characterized by a high morbidity and recurrence rate, primarily attributed to metabolic disorders. The identification of more metabolic biomarkers would provide valuable insights into the etiology of stone formation and the assessment of disease risk. The present study aimed to seek potential organic acid (OA) biomarkers from morning urine samples and explore new methods based on machine learning (ML) for metabolic risk prediction of urolithiasis.

METHODS

Morning urine samples were collected from 117 healthy controls and 156 urolithiasis patients. Gas chromatography-mass spectrometry was used to obtain metabolic profiles. Principal component analysis and ML were carried out to screen robust markers and establish a prediction evaluation model.

RESULTS

There were 25 differential metabolites identified, such as palmitic acid, l-pyroglutamic acid, glyoxylate, and ketoglutarate, mainly involving arginine and proline metabolism, fatty acid degradation, glycine, serine, and threonine metabolism, glyoxylate and dicarboxylic acid metabolism. The urinary OA markers significantly improved the performance of the ML model. The sensitivity and specificity were up to 87.50% and 84.38%, respectively. The area under the receiver operating characteristic curve (AUC) was significantly improved (AUC = 0.9248).

CONCLUSION

The results suggest that OA profiles in morning urine can improve the accuracy of predicting urolithiasis risk and possibly help understand the involvement of metabolic perturbations in metabolic pathways of stone formation and to provide new insights.

Serum metabolomics study reveals a distinct metabolic diagnostic model for renal calculi

Renal calculi (RC) represent a prevalent disease of the urinary system characterized by a high incidence rate. The traditional clinical diagnosis of RC emphasizes imaging and stone composition analysis. However, the significance of metabolic status in RC diagnosis and prevention remains unclear. This study aimed to investigate serum metabolites in RC patients to identify those associated with RC and to develop a metabolite-based diagnostic model. We employed nontargeted metabolomics utilizing ultra-performance liquid chromatography‒mass spectrometry (UPLC‒MS) to compare serum metabolites between RC patients and healthy controls. Our findings demonstrated significant disparities in serum metabolites, particularly in fatty acids and glycerophospholipids, between the two groups. Notably, the glycerophospholipid (GP) metabolic pathway in RC patients was significantly disrupted. Logistic regression models using differentially abundant metabolites revealed that elevated levels of 2-butyl-4-methyl phenol and reduced levels of phosphatidylethanolamine (P-16:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z)) had the most substantial effect on RC risk. Overall, our study indicates that RC induces notable alterations in serum metabolites and that the diagnostic model based on these metabolites effectively distinguishes RC. This research offers promising insights and directions for further diagnostic and mechanistic studies on RC.

Normative Data on Serum and Plasma Tryptophan and Kynurenine Concentrations from 8089 Individuals Across 120 Studies: A Systematic Review and Meta-Analysis

In this systematic review and meta-analysis, a normative dataset is generated from the published literature on the kynurenine pathway in control participants extracted from case-control and methodological validation studies. Study characteristics were mapped, and studies were evaluated in terms of analytical rigour and methodological validation. Meta-analyses of variance between types of instruments, sample matrices and metabolites were conducted. Regression analyses were applied to determine the relationship between metabolite, sample matrix, biological sex, participant age and study age. The grand mean concentrations of tryptophan in the serum and plasma were 60.52 ± 15.38 μM and 51.45 ± 10.47 μM, respectively. The grand mean concentrations of kynurenine in the serum and plasma were 1.96 ± 0.51 μM and 1.82 ± 0.54 μM, respectively. Regional differences in metabolite concentrations were observed across America, Asia, Australia, Europe and the Middle East. Of the total variance within the data, mode of detection (MOD) accounted for up to 2.96%, sample matrix up to 3.23%, and their interaction explained up to 1.53%; the latter of which was determined to be negligible. This review was intended to inform future empirical research and method development studies and successfully synthesised pilot data. The pilot data reported in this study will inform future precision medicine initiatives aimed at targeting the kynurenine pathway by improving the availability and quality of normative data.

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.

A Metabolic Signature of Hereditary Transthyretin Amyloidosis: A Pilot Study

Hereditary transthyretin amyloidosis is the most common form of hereditary amyloidosis, with an autosomal dominant inheritance and a variable penetrance. ATTRv amyloidosis can present as a progressive, axonal sensory autonomic and motor neuropathy or as an infiltrative cardiomyopathy. The definition of biomarkers for the early diagnosis of ATTRv is particularly important in the current era of emerging treatments. In this sense, metabolomics could be an instrument able to provide metabolic profiles with their related metabolic pathways, and we would propose them as possible fluid biomarkers. The aim of this study is to identify altered metabolites (free fatty acids and amino acids) in subjects with a confirmed pathogenic TTR variant. Out of the studied total free fatty acids and amino acids, the serum values of palmitic acid are significantly lower in the ATTRv patients compared to the recruited healthy subjects. The metabolic remodeling identified in this neurogenetic disorder could be the manifestation of pathophysiological processes of the disease, such as mitochondrial dysfunction and neuroinflammation, and contribute to explaining some of its clinical manifestations.

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.