Fourier transform infrared spectroscopy for analysis of kidney stones

Advancements in stone classification: unveiling the beauty of urolithiasis

PURPOSE

Urolithiasis has become increasingly prevalent, leading to higher disability-adjusted life years and deaths. Various stone classification systems have been developed to enhance the understanding of lithogenesis, aid urologists in treatment decisions, and predict recurrence risk. The aim of this manuscript is to provide an overview of different stone classification criteria.

METHODS

Two authors conducted a review of literature on studies relating to the classification of urolithiasis. A narrative synthesis for analysis of the studies was used.

RESULTS

Stones can be categorized based on anatomical position, size, medical imaging features, risk of recurrence, etiology, composition, and morphoconstitutional analysis. The first three mentioned offer a straightforward approach to stone classification, directly influencing treatment recommendations. With the routine use of CT imaging before treatment, precise details like anatomical location, stone dimensions, and Hounsfield Units can be easily determined, aiding treatment planning. In contrast, classifying stones based on risk of recurrence and etiology is more complex due to dependencies on multiple variables, including stone composition and morphology. A classification system based on morphoconstitutional analysis, which combines morphological stone appearance and chemical composition, has demonstrated its value. It allows for the rapid identification of crystalline phase principles, the detection of crystalline conversion processes, the determination of etiopathogenesis, the recognition of lithogenic processes, the assessment of crystal formation speed, related recurrence rates, and guidance for selecting appropriate treatment modalities.

CONCLUSIONS

Recognizing that no single classification system can comprehensively cover all aspects, the integration of all classification approaches is essential for tailoring urolithiasis patient-specific management.

Environmental Conditions as Determinants of Kidney Stone Formation

Urolithiasis is a disease characterized by the presence of stones in the urinary tract, whether in the kidneys, ureters, or bladder. Its origin is multiple, and causes can be cited as hereditary, environmental, dietary, anatomical, metabolic, or infectious factors. A kidney stone is a biomaterial that originates inside the urinary tract, following the principles of crystalline growth, and in most cases, it cannot be eliminated naturally. In this work, 40 calculi from the Don Benito, Badajoz University Hospital are studied and compared with those collected in Madrid to establish differences between both populations with the same pathology and located in very different geographical areas. Analysis by cathodoluminescence offers information on the low crystallinity of the phases and their hydration states, as well as the importance of the bonds with the Ca cation in all of the structures, which, in turn, is related to environmental and social factors of different population groups such as a high intake of proteins, medications, bacterial factors, or possible contamination with greenhouse gases, among other factors.

Chemical Studies of Multicomponent Kidney Stones Using the Modern Advanced Research Methods

Defining the kidney stone composition is important for determining a treatment plan, understanding etiology and preventing recurrence of nephrolithiasis, which is considered as a common, civilization disease and a serious worldwide medical problem. The aim of this study was to investigate the morphology and chemical composition of multicomponent kidney stones. The identification methods such as infrared spectroscopy (FTIR), X-ray diffraction (XRD), and electron microscopy with the EDX detector were presented. The studies by the X-ray photoelectron spectroscopy (XPS) were also carried out for better understanding of their chemical structure. The chemical mapping by the FTIR microscopy was performed to show the distribution of individual chemical compounds that constitute the building blocks of kidney stones. The use of modern research methods with a particular emphasis on the spectroscopic methods allowed for a thorough examination of the subject of nephrolithiasis.

Carboxymethylated Rhizoma alismatis Polysaccharides Regulate Calcium Oxalate Crystals Growth and Reduce the Regulated Crystals' Cytotoxicity

OBJECTIVE

This study explored the effects of polysaccharides (RAPD) extracted from the traditional anti-stone Chinese medicine Rhizoma alismatis and their carboxymethylated derivatives (RAPs) on the crystal phase, morphology, and size of calcium oxalate (CaOx). It also determined the damaging ability of the regulated crystals on human renal tubular epithelial cells (HK-2).

METHODS

RAPD carboxymethylation with a carboxyl group (-COOH) content of 3.57% was carried out by the chloroacetic acid solvent method. The effects of -COOH content in RAPs and RAP concentration on the regulation of CaOx crystal growth were studied by controlling the variables. Cell experiments were conducted to explore the differences in the cytotoxicity of RAP-regulated crystals.

RESULTS

The -COOH contents of RAPD, RAP1, RAP2, and RAP3 were 3.57%, 7.79%, 10.84%, and 15.33%, respectively. RAPs can inhibit the growth of calcium oxalate monohydrate (COM) and induce the formation of calcium oxalate dihydrate (COD). When the -COOH content in RAPs was high, their ability to induce COD formation was enhanced. In the crystals induced by RAPs, a high COD content can lower the damage to cells. In particular, the cytotoxicity of the crystals induced by RAP3 was the lowest. When the concentration of RAP3 increased, the cytotoxicity gradually increased due to the reduced size of the formed COD crystals. An interaction was observed between RAPs and crystals, and the number of RAPs adsorbed in the crystals was positively correlated with the -COOH content in RAPs.

CONCLUSIONS

RAPs can reduce the damage of CaOx to HK-2 cells by regulating the crystallization of CaOx crystals and effectively reducing the risk of kidney stone formation. RAPs, especially RAP3 with a high carboxyl group content, has the potential to be developed as a novel green anti-stone drug.

Autofluorescence spectral analysis for detecting urinary stone composition in emulated intraoperative ambient

The prevalence and disease burden of urolithiasis has increased substantially worldwide in the last decade, and intraluminal holmium laser lithotripsy has become the primary treatment method. However, inappropriate laser energy settings increase the risk of perioperative complications, largely due to the lack of intraoperative information on the stone composition, which determines the stone melting point. To address this issue, we developed a fiber-based fluorescence spectrometry method that detects and classifies the autofluorescence spectral fingerprints of urinary stones into three categories: calcium oxalate, uric acid, and struvite. By applying the support vector machine (SVM), the prediction accuracy achieved 90.28 % and 96.70% for classifying calcium stones versus non-calcium stones and uric acid versus struvite, respectively. High accuracy and specificity were achieved for a wide range of working distances and angles between the fiber tip and stone surface in an emulated intraoperative ambient. Our work establishes the methodological basis for engineering a clinical device that achieves real-time, in situ classification of urinary stones for optimizing the laser ablation parameters and reducing perioperative complications in lithotripsy.

Expression Optimizing of Recombinant Oxalyl-CoA Decarboxylase in Escherichia coli

Background

One of the most common diseases of the urinary tract is stones of this system, including kidney stones. About 70%-80% of kidney stones are calcium oxalate. Oxalyl-CoA decarboxylase is a single polypeptide included of 568 amino acids which play a key role in oxalate degradation.

Materials and Methods

The aim of current study is high-level expression of oxalyl-CoA decarboxylase in Escherichia coli BL21 (DE3). To achieve this aim, oxalyl-CoA decarboxylase gene was cloned upon pET-30a (+) with T7 promoter. The vector containing the oxalyl-CoA decarboxylase gene was transformed into E. coli and the expression of the gene was examined on a laboratory scale and fermentor. Atfirst, the effect of temperature, culture medium, and induction time on oxalyl-CoA decarboxylase expression at three levels was examined.

Results

The obtained data showed that the highest expression was related to the terrific broth culture medium and temperature of 32°C with an inducer concentration of 1 mM. Under this situation the ultimate cells dry weight and the final oxalyl-CoA decarboxylase expression were 2.46 g/l and 36% of total protein, respectively. Then induction time was optimized in a bench bioreactor and productivity of oxalyl-CoA decarboxylase was calculated. Under optimized condition the cell density, biomass productivity and oxalyl-CoA decarboxylase concentration reached 4.02 g/l, 0.22 g/l/h, and 0.7 g/l which are one of the highest reported rates.

Conclusion

This study demonstrated that high levels of oxalyl-CoA decarboxylase can be achieved by optimizing the expression conditions.

Development and validation of standard and real patient gallstone library using Fourier transform infra-red spectroscopy

Background

Analysis of the constituents of gallstones using various spectroscopic techniques assists in identification of the pathogenesis of gallstones. In the current study, using Fourier Transform Infra-Red (FTIR) Spectroscopy, a Gallstone Standard Library (GSL) and a Gallstone Real Patients’ Library (GRPL) were developed and validated for gallstone composition analysis.

Methods

The study was conducted at the Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan. Pure standards (cholesterol, calcium carbonate, bilirubin and bile salts) and gallstone specimens were analyzed using FTIR Nicolet iS-5 Spectrometer from Thermo Fisher Scientific, USA. Thermo Scientific™ QCheck™ algorithm, embedded within the OMNIC™ software, was used to identify the unique spectral fingerprint of the patient samples to match with known, standard material. Matching of > 75% was considered acceptable. Validation for accuracy of the library was performed for twenty analyzed gallstones at an international reference lab.

Results

Concerted search analysis was performed against the developed GSL consisting of 71 “pure component” spectrum divided into 5 types to generate the library. For the Gallstone Real Patient Library (GRPL), 117 patient samples were analyzed. Ninety-eight gall stones (83.8%) out of 117 stones matched with the developed GSL. Majority stones were mixed stones (95.92%), with cholesterol being the primary component (91.83%). Results of the developed library were 100% in agreement with the reports received from the external reference lab.

Conclusions

The library developed displayed good consistency and can be used for detection of gallstone composition in Pakistan and replace the traditional labor- and time-intensive chemical method of gallstone analysis.

Validation of the infrared spectroscopy method for analysis of the composition of urine concretes

The aim of this study was to validate the method for analyzing the composition of calculus using infrared (IR) spectroscopy by studying model mixtures of salts. Study was made with an ALPHA-P IR Fourier spectrometer with OPUS software (Bruker, Germany). The samples of pure chemical salts manufactured by Sigma-Aldrich USA were used to validate the method. Salt mixtures were prepared in ratios of 10/90, 50/50 and 90/10. To assess the effect of the fraction size on the calculus component results, were used calculi of patients with urolithiasis. For each mixture were used 10 repeated measurements. Analysis of the composition of model salts showed that in the study of pure cystine salt CV(%) was 0,79%, calcium carbonate - 0,92%, sodium urate - 0,97%, calcium oxalate monohydrate - 4,94%, magnesium ammonium phosphate - 5,59%. And the most common components were analyzed in the composition of complex mixtures, including 90%, 50% and 10% of the investigated component. Calcium oxalate monohydrate has CV(%) 5.70% in mixture 9 part of it to one part of impurities, in mixture 50/50 - 21.57% and in 10/90 - 5.70%. For uric acid in 90/10 - 2.20%, in 50/50 - 10.09%, in 10/90 - 31.94%. For calcium carbonate in 90/10 - 9.02%, in 50/50 - 11.98%, in 10/90 - 24.70%. The dispersion analysis showed that the weighed portions of salts with a particle diameter of more than 0.8 mm provide reproducibility with a CV - 11.48%, with a diameter of 0.2-0.8 mm - 5.35%, and finally less than 0.1 mm - 2.28%. The accuracy of the method is high, but the reproducibility of the IR-spectroscopy method is relatively low in the analysis of stones of mixed composition, due to the greater error in the determination of impurities. Laboratories should pay special attention to optimizing sample preparation to ensure particle fineness less than 0.1 mm.

Composition of Uroliths seen in patients in Abuja, Nigeria: a single centre retrospective analysis of 155 stones

Background

Uroliths are stones formed in the urinary tract. Analysis of stones helps to identify risk factors for their development and prevention of recurrence. Standard stone analysis using modern technology is not routinely done in Nigeria. This study sought to determine the chemical composition of urinary stones seen in Abuja, Nigeria.

Methods

This was a retrospective study on composition of uroliths. Urinary stones surgically removed from 155 patients through minimal access surgical procedures between January 2015 and August 2019 were analysed. Optical crystallography and infrared spectroscopy were used to determine the chemical composition of the urinary stones.

Results

A total of 155 urinary stones were assembled from the patients. More stones were removed from male patients and the male to female ratio was 1.9:1. Stones were rare in the extremes of age. The predominant location (89.7%) of stones was in the upper urinary tract. All stones were of mixed composition with calcium oxalate accounting for 93.55%. Calcium oxalate, calcium phosphate and uric acid stones were more common in the upper tract, while 2 of the 3 struvite stones were found in the lower tract.

Conclusion

Stones found in this study were of mixed composition with the most common constituent being Calcium oxalate and the least common, struvite.

Correlations between stones composition, dietary and comorbidities context of the lithiasic patient

The incidence of nephrolithiasis is in full expansion, its etiology being frequently associated with lifestyle changes. The objective of this retrospective study, carried out between April and December 2019, was to identify the correlations of the known lithogenic factors with the chemical structure of the calculi in the patients from the North-Eastern region of Romania. The results obtained after the data analysis of our LAMPA questionnaire (L – liquids, A – antecedents, M – medication, P – associated pathologies, A – aliments) made in evidence a statistically relevant relationship between the heredocollateral history of lithiasis and calcium oxalate dihydrate (COD) calculi, hypertension and calcium oxalate monohydrate (COM) stones, uric lithiasis and diabetes, COD, and obesity, between predominantly uric lithiasis and meat or meat-derived products consumption, between frequent potato consumption and COD stones and the frequently consume of dairy products and predominantly COM calculi. The authors concluded that the use of a complex questionnaire, like LAMPA, together with Fourier-transform infrared (FTIR) spectroscopic and morphological analysis are essential steps for developing an efficient metaphylaxis.

Distinguishing active from quiescent disease in ANCA-associated vasculitis using attenuated total reflection Fourier-transform infrared spectroscopy

The current lack of a reliable biomarker of disease activity in anti-neutrophil cytoplasmic autoantibody (ANCA) associated vasculitis poses a significant clinical unmet need when determining relapsing or persisting disease. In this study, we demonstrate for the first time that attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy offers a novel and functional candidate biomarker, distinguishing active from quiescent disease with a high degree of accuracy. Paired blood and urine samples were collected within a single UK centre from patients with active disease, disease remission, disease controls and healthy controls. Three key biofluids were evaluated; plasma, serum and urine, with subsequent chemometric analysis and blind predictive model validation. Spectrochemical interrogation proved plasma to be the most conducive biofluid, with excellent separation between the two categories on PC2 direction (AUC 0.901) and 100% sensitivity (F-score 92.3%) for disease remission and 85.7% specificity (F-score 92.3%) for active disease on blind predictive modelling. This was independent of organ system involvement and current ANCA status, with similar findings observed on comparative analysis following successful remission-induction therapy (AUC > 0.9, 100% sensitivity for disease remission, F-score 75%). This promising technique is clinically translatable and warrants future larger study with longitudinal data, potentially aiding earlier intervention and individualisation of treatment.

Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) detection as a rapid and convenient screening test for cystinuria

BACKGROUND

Cystinuria is an inborn congenital disorder characterised by a defective cystine metabolism resulting in the formation of cystine stones. The Brand's test, used for diagnosis, requires dangerous substances, so has been replaced with high-performance liquid chromatography with fluorimetric detection (HPLC-FL). However, this technique requires the use of complex equipment. Infrared spectroscopy, universally used for stone analysis, recently was employed to detect insoluble cystine in urine. The aim of this study is to evaluate Infrared Spectroscopy combined with chemometric analysis as screening method to identify those patients requiring confirmation by HPLC-FL analysis.

METHODS

We examined 24 h urine specimens from 57 patients. The quantitative analysis was performed by HPLC-FL. The infrared spectroscopic urine sediment analysis was performed with an ATR accessory (ATR-FTIR). Urine is centrifuged, the supernatant is discarded, and the sediment is dried on to the ATR prism surface. Statistical analysis was performed using a custom-made software developed in MATLAB environment.

RESULTS

The HPLC-FL determination showed a normal excretion of cystine in 49 samples and an abnormal excretion in the remaining 8 samples. The ATR-FTIR analysis combined with a statistical approach gives a sensitivity of 1.0 and a specificity of 0.82 were obtained.

CONCLUSIONS

The introduction of the ATR-FTIR technique in our clinical laboratory setting may reduce time and cost analysis for diagnosis of cystinuria.

Urinary stone composition analysis and clinical characterization of 1520 patients in central China

A total of 1520 patients with urinary stones from central China were collected and analysed by Fourier transform infrared spectroscopy between October 1, 2016 and December 31, 2019. For all patients, age, sex, comorbidities, stone location, laboratory examination and geographic region were collected. The most common stone component was calcium oxalate (77.5%), followed by calcium phosphate (8.7%), infection stone (7.6%), uric acid (UA) stone (5.3%)and cystine (0.9%). The males had more calcium oxalate stones (p < 0.001), while infection stone and cystine stones occurred more frequently in females (p < 0.001). The prevalence peak occurred at 41-60 years in both men and women. UA stones occurred frequently in patients with lower urinary pH (p < 0.001), while neutral urine or alkaline urine (p < 0.001) and urinary infection (p < 0.001) were more likely to be associated with infection stone stones. Patients with high levels of serum creatinine were more likely to develop UA stones (p < 0.001). The proportion of UA stones in diabetics was higher (p < 0.001), and the incidence of hypertension was higher in patients with UA stones (p < 0.001). Compared to the other types, more calcium oxalate stones were detected in the kidneys and ureters (p < 0.001), whereas struvite stones were more frequently observed in the lower urinary tract (p = 0.001). There was no significant difference in stone composition across the Qinling-Huaihe line in central China except UA stones, which were more frequently observed in patients south of the line (p < 0.001).

Analysis of stones formed in the human gall bladder and kidney using advanced spectroscopic techniques

Stone diseases (gallstones and kidney stones) are extremely painful and often cause death. The prime aim of biomedical research in this area has been determination of factors resulting in stone formation inside the gallbladder and urinary tract. Many theories have been put forward to explain the mechanism of stone formation and their growth; however, their complete cycle of pathogenesis is still under debate. Several factors are responsible for stone formation; however, much emphasis is placed on the determination of elemental and molecular composition of the stones. In the present review article, we describe different kinds of spectroscopic techniques such as Fourier transform infrared spectroscopy (FTIR), X-ray fluorescence (XRF) spectroscopy, time-of-flight secondary ion mass spectrometry (TOF-SIMS), and laser-induced breakdown spectroscopy (LIBS) and highlight their use in the analysis of stone diseases. We have summarized work done on gallstones and kidney stones using these advanced techniques particularly over the last 10 years. We have also briefly elaborated the basics of stone formations inside the human body and their complications for a better understanding of the subject.

The effect of the body mass index on the types of urinary tract stones

Objectives:

Urinary tract stones are a common public health problem worldwide. In addition, identifying the composition of stones is important for the further metabolic evaluation of patients. We conducted this study to further correlate the relationship between body mass index (BMI) and different compositions of urinary tract stones.

Materials and Methods:

A retrospective study of 433 patients who underwent urinary tract stone analysis via Fourier-transform infrared spectroscopy at King Khalid University Hospital in Riyadh from May 2015 to June 2017 was performed. Their BMI at the time of stone analysis was recorded.

Results:

A total of 433 stones were analyzed by the statistical data analysis software. The BMI was classified according to the WHO classification. We divided our patients into seven age groups. Most patients were between the age group of 35 and 44 years and were overweight. The incidence of calcium oxalate, carbonate apatite, and uric acid stones was higher in patients with a BMI above thirty than in patients with a lower BMI. However, cystine stones were more common in normal-weight patients.

Conclusions:

In this study, we found that the incidence of certain types of stones, such as calcium oxalate, cystine, and uric acid stones, in Saudi Arabia can be predicted by BMI measurement.

Exploring the Therapeutic Mechanism of Desmodium styracifolium on Oxalate Crystal-Induced Kidney Injuries Using Comprehensive Approaches Based on Proteomics and Network Pharmacology

Purpose: As a Chinese medicinal herb, Desmodium styracifolium (Osb.) Merr (DS) has been applied clinically to alleviate crystal-induced kidney injuries, but its effective components and their specific mechanisms still need further exploration. This research first combined the methods of network pharmacology and proteomics to explore the therapeutic protein targets of DS on oxalate crystal-induced kidney injuries to provide a reference for relevant clinical use.

Methods: Oxalate-induced kidney injury mouse, rat, and HK-2 cell models were established. Proteins differentially expressed between the oxalate and control groups were respectively screened using iTRAQ combined with MALDI-TOF-MS. The common differential proteins of the three models were further analyzed by molecular docking with DS compounds to acquire differential targets. The inverse docking targets of DS were predicted through the platform of PharmMapper. The protein–protein interaction (PPI) relationship between the inverse docking targets and the differential proteins was established by STRING. Potential targets were further validated by western blot based on a mouse model with DS treatment. The effects of constituent compounds, including luteolin, apigenin, and genistein, were investigated based on an oxalate-stimulated HK-2 cell model.

Results: Thirty-six common differentially expressed proteins were identified by proteomic analysis. According to previous research, the 3D structures of 15 major constituents of DS were acquired. Nineteen differential targets, including cathepsin D (CTSD), were found using molecular docking, and the component-differential target network was established. Inverse-docking targets including p38 MAPK and CDK-2 were found, and the network of component-reverse docking target was established. Through PPI analysis, 17 inverse-docking targets were linked to differential proteins. The combined network of component-inverse docking target-differential proteins was then constructed. The expressions of CTSD, p-p38 MAPK, and p-CDK-2 were shown to be increased in the oxalate group and decreased in kidney tissue by the DS treatment. Luteolin, apigenin, and genistein could protect oxalate-stimulated tubular cells as active components of DS.

Conclusion: The potential targets including the CTSD, p38 MAPK, and CDK2 of DS in oxalate-induced kidney injuries and the active components (luteolin, apigenin, and genistein) of DS were successfully identified in this study by combining proteomics analysis, network pharmacology prediction, and experimental validation.