Geobiology reveals how human kidney stones dissolve in vivo

Risk Factors of Asymptomatic Kidney Stone Passage in Adults with Recurrent Kidney Stones

Key Points

Background

Kidney stones are a common health problem and are characterized by a high risk of recurrence. A certain number of kidney stones pass asymptomatically. Data regarding the frequency of asymptomatic spontaneous stone passages are limited.

Methods

To assess the frequency of asymptomatic spontaneous stone passage and its covariates, we conducted a post hoc analysis of the prospective randomized NOSTONE trial. All asymptomatic spontaneous stone passages were identified by comparing the total number of kidney stones on low-dose noncontrast computed tomography (CT) imaging at the beginning and end of the study, considering symptomatic stone passages and surgical stone removal. The statistical analysis focused on the association of independent variables and the number of asymptomatic spontaneous stone passages using linear regression analyses.

Results

Of the 416 randomized patients, 383 with both baseline and end-of-study CT were included in this analysis. The median follow-up period was 35 months, the median patient age was 49 years (interquartile range [IQR], 40–55), and 20% of the patients were female. A total of 442 stone events occurred in 209 of 383 (55%) patients: 217 of 442 (49%) were symptomatic spontaneous stone passages, 67 of 442 (15%) were surgically removed stones, and 158 of 442 (36%) were asymptomatic spontaneous stone passages. The median size of asymptomatic stones (2.4 mm; IQR, 1.95–3.4) and the size of symptomatic stones (2.15 mm; IQR, 1.68–2.79) that passed spontaneously were not significantly different (P = 0.37). The number of asymptomatic spontaneous stone passages was significantly associated with a higher number of stones on CT at randomization (P = 0.001). Limitations include the lack of data on stone size at the time of passage and overrepresentation of White men.

Conclusions

Asymptomatic stone passage was common in patients with recurrent calcium-containing kidney stones. The higher the number of stones at presentation, the more likely it was that a kidney stone would spontaneously pass over time without causing any symptoms.

Clinical Trial registry name and registration number:

NOSTONE trial and: NCT03057431.

Osteopontin stabilization and collagen containment slows amorphous calcium phosphate transformation during human aortic valve leaflet calcification

Calcification of aortic valve leaflets is a growing mortality threat for the 18 million human lives claimed globally each year by heart disease. Extensive research has focused on the cellular and molecular pathophysiology associated with calcification, yet the detailed composition, structure, distribution and etiological history of mineral deposition remains unknown. Here transdisciplinary geology, biology and medicine (GeoBioMed) approaches prove that leaflet calcification is driven by amorphous calcium phosphate (ACP), ACP at the threshold of transformation toward hydroxyapatite (HAP) and cholesterol biomineralization. A paragenetic sequence of events is observed that includes: (1) original formation of unaltered leaflet tissues: (2) individual and coalescing 100's nm- to 1 μm-scale ACP spherules and cholesterol crystals biomineralizing collagen fibers and smooth muscle cell myofilaments; (3) osteopontin coatings that stabilize ACP and collagen containment of nodules preventing exposure to the solution chemistry and water content of pumping blood, which combine to slow transformation to HAP; (4) mm-scale nodule growth via ACP spherule coalescence, diagenetic incorporation of altered collagen and aggregation with other ACP nodules; and (5) leaflet diastole and systole flexure causing nodules to twist, fold their encasing collagen fibers and increase stiffness. These in vivo mechanisms combine to slow leaflet calcification and establish previously unexplored hypotheses for testing novel drug therapies and clinical interventions as viable alternatives to current reliance on surgical/percutaneous valve implants.

Kidney stone growth through the lens of Raman mapping

Bulk composition of kidney stones, often analyzed with infrared spectroscopy, plays an essential role in determining the course of treatment for kidney stone disease. Though bulk analysis of kidney stones can hint at the general causes of stone formation, it is necessary to understand kidney stone microstructure to further advance potential treatments that rely on in vivo dissolution of stones rather than surgery. The utility of Raman microscopy is demonstrated for the purpose of studying kidney stone microstructure with chemical maps at ≤ 1 µm scales collected for calcium oxalate, calcium phosphate, uric acid, and struvite stones. Observed microstructures are discussed with respect to kidney stone growth and dissolution with emphasis placed on < 5 µm features that would be difficult to identify using alternative techniques including micro computed tomography. These features include thin concentric rings of calcium oxalate monohydrate within uric acid stones and increased frequency of calcium oxalate crystals within regions of elongated crystal growth in a brushite stone. We relate these observations to potential concerns of clinical significance including dissolution of uric acid by raising urine pH and the higher rates of brushite stone recurrence compared to other non-infectious kidney stones.

The impact of crystal phase transition on the hardness and structure of kidney stones

Calcium oxalate kidney stones, the most prevalent type of kidney stones, undergo a multi-step process of crystal nucleation, growth, aggregation, and secondary transition. The secondary transition has been rather overlooked, and thus, the effects on the disease and the underlying mechanism remain unclear. Here, we show, by periodic micro-CT images of human kidney stones in an ex vivo incubation experiment, that the growth of porous aggregates of calcium oxalate dihydrate (COD) crystals triggers the hardening of the kidney stones that causes difficulty in lithotripsy of kidney stone disease in the secondary transition. This hardening was caused by the internal nucleation and growth of precise calcium oxalate monohydrate (COM) crystals from isolated urine in which the calcium oxalate concentrations decreased by the growth of COD in closed grain boundaries of COD aggregate kidney stones. Reducing the calcium oxalate concentrations in urine is regarded as a typical approach for avoiding the recurrence. However, our results revealed that the decrease of the concentrations in closed microenvironments conversely promotes the transition of the COD aggregates into hard COM aggregates. We anticipate that the suppression of the secondary transition has the potential to manage the deterioration of kidney stone disease.

Layered structure of sialoliths compared with tonsilloliths and antroliths

Objectives

The aim of this study was to perform a comparative analysis of the ultrastructural and chemical composition of sialoliths, tonsilloliths, and antroliths and to describe their growth pattern.

Materials and Methods

We obtained 19 specimens from 18 patients and classified the specimens into three groups: sialolith (A), tonsillolith (B), and antrolith (C). The peripheral, middle, and core regions of the specimens were examined in detail by histology, micro-computed tomography (micro- CT), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy, and transmission electron microscopy (TEM).

Results

In the micro-CT, group A showed alternating radiodense and radiolucent layers, while group B had a homogeneous structure. Group C specimens revealed a compact homogeneous structure. Histopathologically, group A showed a laminated, teardrop-shaped, globular structure. Group B demonstrated degrees of immature calcification of organic and inorganic materials. In group C, the lesion was not encapsulated and showed a homogeneous lamellar bone structure. SEM revealed that group A showed distinct three layers: a peripheral multilayer zone, intermediate compact zone, and the central nidus area; groups B and C did not show these layers. The main elemental components of sialoliths were O, C, Ca, N, Cu, P, Zn, Si, Zr, F, Na, and Mg. In group B, a small amount of Fe was found in the peripheral region. Group C had a shorter component list: Ca, C, O, P, F, N, Si, Na, and Mg. TEM analysis of group A showed globular structures undergoing intra-vesicular calcification. In group B, bacteria were present in the middle layer. In the outer layer of the group C antrolith, an osteoblastic rimming was observed.

Conclusion

Sialoliths had distinct three layers: a peripheral multilayer zone, an intermediate compact zone and the central nidus area, while the tonsillolith and antrolith specimens lacked distinct layers and a core.

Identification of biological components for sialolith formation organized in circular multi-layers

According to the previous studies of sialolithiasis reported so far, this study is aimed to identify the biological components of sialolith, which show different ultrastructures and chemical compositions from other stones, cholelith and urolith. Twenty-two specimens obtained from 20 patients were examined histologically, and analyzed with micro-CT, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), and transmission electron microscopy (TEM). All sialoliths (n = 22) observed in this study showed a central nidus, which was filled with organoid matrix admixed with exosome vesicles, loose calcium apatite crystals, and many bacteria. The micro-CT and SEM observation clearly defined a single or multiple central nidus(es) encircled by highly calcified compact zone. The circular compact zone showed a band-like calcification, about 1-3 mm in thickness, and usually located between the central nidus and the peripheral multilayer zone. But some sialoliths (n = 5) showed severe erosion of compact zone by expanding multilayered zone depending on the level of calcification and inflammation in sialolith. By observing TEM images, many exosome vesicles and degraded cytoplasmic organelles were found in the central nidus, and some epithelial cells were also found in the calcified matrix of peripheral multilayer zone. Particularly, EDS analysis indicated the highest Ca/P ratio in the intermediate compact zone (1.77), and followed by the central nidus area (1.39) and the peripheral multilayer zone (0.87). Taken together, these data suggest that the central nidus containing many inflammatory exosomes and degraded cytoplasmic organelles has a potential to induce a band-like calcification of compact zone, and followed by the additional multilayer deposition of exfoliated salivary epithelial cells as well as salivary materials. Thereby, the calcium apatite-based sialolith is gradually growing in its volume size, and eventually obstructs the salivary flow and provides a site for the bacterial infection.

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.

ePHex: a phase 3, double-blind, placebo-controlled, randomized study to evaluate long-term efficacy and safety of Oxalobacter formigenes in patients with primary hyperoxaluria

BACKGROUND

Primary hyperoxalurias (PHs) are rare genetic diseases that increase the endogenous level of oxalate, a waste metabolite excreted predominantly by the kidneys and also the gut. Treatments aim to improve oxalate excretion, or reduce oxalate generation, to prevent kidney function deterioration. Oxalobacter formigenes is an oxalate metabolizing bacterium. This Phase III, double-blind, placebo-controlled randomized trial investigated the effectiveness of orally administered Oxabact™, a lyophilized O. formigenes formulation, at reducing plasma oxalate levels in patients suffering from PH.

METHODS

Subjects (≥ 2 years of age) with a diagnosis of PH and maintained but suboptimal kidney function (mean estimated glomerular filtration rate at baseline < 90 mL/min/1.73 m²) were eligible to participate. Subjects were randomized to receive Oxabact or placebo twice daily for 52 weeks. Change from baseline in plasma oxalate concentration at Week 52 was the primary study endpoint.

RESULTS

Forty-three subjects were screened, 25 were recruited and one was discontinued. At Week 52, O. formigenes was established in the gut of subjects receiving Oxabact. Despite decreasing plasma oxalate level in subjects treated with Oxabact, and stable/increased levels with placebo, there was no significant difference between groups in the primary outcome (Least Squares mean estimate of treatment difference was - 3.80 μmol/L; 95% CI: - 7.83, 0.23; p-value = 0.064). Kidney function remained stable in both treatments.

CONCLUSIONS

Oxabact treatment may have stabilized/reduced plasma oxalate versus a rise with placebo, but the difference over 12 months was not statistically significant (p = 0.06). A subtle effect observed with Oxabact suggests that O. formigenes may aid in preventing kidney stones. A higher resolution version of the Graphical abstract is available as Supplementary information.

Quantitative analysis of calcium oxalate monohydrate and dihydrate for elucidating the formation mechanism of calcium oxalate kidney stones

We sought to identify and quantitatively analyze calcium oxalate (CaOx) kidney stones on the order of micrometers, with a focus on the quantitative identification of calcium oxalate monohydrate (COM) and dihydrate (COD). We performed Fourier transform infrared (FTIR) spectroscopy, powder X-ray diffraction (PXRD), and microfocus X-ray computed tomography measurements (microfocus X-ray CT) and compared their results. An extended analysis of the FTIR spectrum focusing on the 780 cm-1 peak made it possible to achieve a reliable analysis of the COM/COD ratio. We succeeded in the quantitative analysis of COM/COD in 50-μm2 areas by applying microscopic FTIR for thin sections of kidney stones, and by applying microfocus X-ray CT system for bulk samples. The analysis results based on the PXRD measurements with micro-sampling, the microscopic FTIR analysis of thin sections, and the microfocus X-ray CT system observation of a bulk kidney stone sample showed roughly consistent results, indicating that all three methods can be used complementarily. This quantitative analysis method evaluates the detailed CaOx composition on the preserved stone surface and provides information on the stone formation processes. This information clarifies where and which crystal phase nucleates, how the crystals grow, and how the transition from the metastable phase to the stable phase proceeds. The phase transition affects the growth rate and hardness of kidney stones and thus provides crucial clues to the kidney stone formation process.

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.

GeoBioMed perspectives on kidney stone recurrence from the reactive surface area of SWL-derived particles

Shock wave lithotripsy (SWL) is an effective and commonly applied clinical treatment for human kidney stones. Yet the success of SWL is counterbalanced by the risk of retained fragments causing recurrent stone formation, which may require retreatment. This study has applied GeoBioMed experimental and analytical approaches to determine the size frequency distribution, fracture patterns, and reactive surface area of SWL-derived particles within the context of their original crystal growth structure (crystalline architecture) as revealed by confocal autofluorescence (CAF) and super-resolution autofluorescence (SRAF) microscopy. Multiple calcium oxalate (CaOx) stones were removed from a Mayo Clinic patient using standard percutaneous nephrolithotomy (PCNL) and shock pulse lithotripsy (SPL). This produced approximately 4-12 mm-diameter PCNL-derived fragments that were experimentally treated ex vivo with SWL to form hundreds of smaller particles. Fractures propagated through the crystalline architecture of PCNL-derived fragments in a variety of geometric orientations to form rectangular, pointed, concentrically spalled, and irregular SWL-derived particles. Size frequency distributions ranged from fine silt (4-8 μm) to very fine pebbles (2-4 mm), according to the Wentworth grain size scale, with a mean size of fine sand (125-250 μm). Importantly, these SWL-derived particles are smaller than the 3-4 mm-diameter detection limit of clinical computed tomography (CT) techniques and can be retained on internal kidney membrane surfaces. This creates clinically undetectable crystallization seed points with extremely high reactive surface areas, which dramatically enhance the multiple events of crystallization and dissolution (diagenetic phase transitions) that may lead to the high rates of CaOx kidney stone recurrence after SWL treatment.

May a comprehensive mineralogical study of a jackstone calculus and some other human bladder stones unveil health and environmental implications?

This paper represents the first result of an active collaboration between the University of Sannio and the San Pio Hospital (Benevento, Italy), started in the 2018, that aims to a detailed mineralogical investigation of urinary stones of patients from Campania region. Herein, selected human bladder stones have been deeply characterized for clinical purposes and environmental biomonitoring, focusing on the importance to evaluate the concentration and distribution of undesired trace elements by means of microscopic techniques in the place of conventional wet chemical analyses. A rare bladder stone with a sea-urchin appearance, known as jackstone calculus, were also investigated (along with bladder stones made of uric acid and brushite) by means a comprehensive analytical approach, including Synchrotron X-ray Diffraction and Simultaneous Thermal Analyses. Main clinical assumptions were inferred according to the morpho-constitutional classification of bladder stones and information about patient's medical history and lifestyle. In most of the analyzed uroliths, undesired trace elements such as copper, cadmium, lead, chromium, mercury and arsenic have been detected and generally attributable to environmental pollution or contaminated food. Simultaneous occurrence of selenium and mercury should denote a methylmercury detoxification process, probably leading to the formation of a very rare HgSe compound known as tiemannite.

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.

Urinary stone composition in Germany: results from 45,783 stone analyses

Purpose

Stone composition can provide valuable information for the diagnosis, treatment and recurrence prevention of urolithiasis. The aim of this study was to evaluate the distribution of urinary stone components and the impact of different crystal forms according to gender and age of patients in Germany.

Methods

A total of 45,783 urinary stones submitted from 32,512 men and 13,271 women between January 2007 and December 2020 were analyzed by infrared spectroscopy. Only the first calculus obtained per patient was included in the analysis.

Results

The most common main stone component was calcium oxalate (CaOx) (71.4%), followed by carbonate apatite (CA) (10.2%) and uric acid (UA) (8.3%). Struvite (2.1%), brushite (1.3%), protein (0.5%) and cystine (0.4%) stones were only rarely diagnosed. CaOx (75%) and UA stones (81%) were more frequently obtained from men than women (p < 0.001). Weddellite (COD) and uric acid dihydrate (UAD) were more common in younger ages than whewellite (COM) and anhydrous uric acid (UAA), respectively, in both men and women. The ratios of COM-to-COD and UAA-to-UAD calculi were approximately 4:1 and 8:1, respectively. The peak of stone occurrence was between the ages of 40 and 59 years.

Conclusion

Stone composition is strongly associated with gender and age. The peak incidence of calculi in both women and men was in the most active phase of their working life. The distinction between different crystal forms could provide clues to the activity and mechanisms of lithogenesis. Further research is needed in understanding the causative factors and the process of stone formation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00345-022-04060-w.

Comparative functional analysis of the urinary tract microbiome for individuals with or without calcium oxalate calculi

Individuals with urinary stone disease (USD) exhibit dysbiosis in the urinary tract and the loss of Lactobacillus that promote urinary tract health. However, the microbial metabolic functions that differentiate individuals with USD from healthy individuals are unknown. The objective of the current study was to determine the microbial functions across prokaryotic, viral, fungal, and protozoan domains that are associated with calcium oxalate (CaOx) stone formers through comparative shotgun metagenomics of midstream, voided urine samples for a small number of patients (n = 5 CaOx stone formers, n = 5 healthy controls). Results revealed that CaOx stone formers had reduced levels of genes associated with oxalate metabolism, as well as transmembrane transport, proteolysis, and oxidation-reduction processes. From 17 draft genomes extracted from the data and > 42,000 full length reference genomes, genes enriched in the Control group mapped overwhelming to Lactobacillus crispatus and those associated with CaOx mapped to Pseudomonas aeruginosa and Burkholderia sp. The microbial functions that differentiated the clinical cohorts are associated with known mechanisms of stone formation. While the prokaryotes most differentiated the CaOx and Control groups, a diverse, trans-domain microbiome was apparent. While our sample numbers were small, results corroborate previous studies and suggest specific microbial metabolic pathways in the urinary tract that modulate stone formation. Future studies that target these metabolic pathways as well as the influence of viruses, fungi, and protozoa on urinary tract physiology is warranted.

Liquid-Liquid Phase Separation in Nucleation Process of Biomineralization

Biomineralization is a typical interdisciplinary subject attracting biologists, chemists, and geologists to figure out its potential mechanism. A mounting number of studies have revealed that the classical nucleation theory is not suitable for all nucleation process of biominerals, and phase-separated structures such as polymer-induced liquid precursors (PILPs) play essential roles in the non-classical nucleation processes. These structures are able to play diverse roles biologically or pathologically, and could also give inspiring clues to bionic applications. However, a lot of confusion and dispute occurred due to the intricacy and interdisciplinary nature of liquid precursors. Researchers in different fields may have different opinions because the terminology and current state of understanding is not common knowledge. As a result, our team reviewed the most recent articles focusing on the nucleation processes of various biominerals to clarify the state-of-the-art understanding of some essential concepts and guide the newcomers to enter this intricate but charming field.

Multicolor imaging of calcium-binding proteins in human kidney stones for elucidating the effects of proteins on crystal growth

The pathogenesis of kidney stone formation includes multi-step processes involving complex interactions between mineral components and protein matrix. Calcium-binding proteins in kidney stones have great influences on the stone formation. The spatial distributions of these proteins in kidney stones are essential for evaluating the in vivo effects of proteins on the stone formation, although the actual distribution of these proteins is still unclear. We reveal micro-scale distributions of three different proteins, namely osteopontin (OPN), renal prothrombin fragment 1 (RPTF-1), and calgranulin A (Cal-A), in human kidney stones retaining original mineral phases and textures: calcium oxalate monohydrate (COM) and calcium oxalate dihydrate (COD). OPN and RPTF-1 were distributed inside of both COM and COD crystals, whereas Cal-A was distributed outside of crystals. OPN and RPTF-1 showed homogeneous distributions in COM crystals with mosaic texture, and periodically distributions parallel to specific crystal faces in COD crystals. The unique distributions of these proteins enable us to interpret the different in vivo effects of each protein on CaOx crystal growth based on their physico-chemical properties and the complex physical environment changes of each protein. This method will further allow us to elucidate in vivo effects of different proteins on kidney stone formation.

Human kidney stones: a natural record of universal biomineralization

GeoBioMed - a new transdisciplinary approach that integrates the fields of geology, biology and medicine - reveals that kidney stones composed of calcium-rich minerals precipitate from a continuum of repeated events of crystallization, dissolution and recrystallization that result from the same fundamental natural processes that have governed billions of years of biomineralization on Earth. This contextual change in our understanding of renal stone formation opens fundamentally new avenues of human kidney stone investigation that include analyses of crystalline structure and stratigraphy, diagenetic phase transitions, and paragenetic sequences across broad length scales from hundreds of nanometres to centimetres (five Powers of 10). This paradigm shift has also enabled the development of a new kidney stone classification scheme according to thermodynamic energetics and crystalline architecture. Evidence suggests that ≥50% of the total volume of individual stones have undergone repeated in vivo dissolution and recrystallization. Amorphous calcium phosphate and hydroxyapatite spherules coalesce to form planar concentric zoning and sector zones that indicate disequilibrium precipitation. In addition, calcium oxalate dihydrate and calcium oxalate monohydrate crystal aggregates exhibit high-frequency organic-matter-rich and mineral-rich nanolayering that is orders of magnitude higher than layering observed in analogous coral reef, Roman aqueduct, cave, deep subsurface and hot-spring deposits. This higher frequency nanolayering represents the unique microenvironment of the kidney in which potent crystallization promoters and inhibitors are working in opposition. These GeoBioMed insights identify previously unexplored strategies for development and testing of new clinical therapies for the prevention and treatment of kidney stones.

Do organic substances act as a degradable binding matrix in calcium oxalate kidney stones?

BACKGROUND

Calcium oxalate (CaOx) stones are considered to be highly resistant to chemolysis. While significant organic matter has been identified within these stones, which is presumed to bind (inorganic) CaOx particles and aggregates, most chemolysis efforts have focused on methods to attack the CaOx components of a stone. We examine the feasibility of inducing chemolysis of CaOx kidney stones, within hours, by specifically attacking the organic matrix present in these stones.

METHODS

In contrast to previous studies, we focused on the possible "brick and mortar" stone configuration. We systematically tested, via in vitro experiments, the ability of an extensive range of 26 potential chemolysis agents to induce relatively fast disintegration (and/or dissolution) of a large set of natural CaOx stone fragments, extracted during endourological procedures, without regard to immediate clinical application. Each stone fragment was monitored for reduction in weight and other changes over 72 h.

RESULTS

We find that agents known to attack organic material have little, if any, effect on stone chemolysis. Similarly, protein and enzymatic agents, and oral additive medical treatments, have little immediate effect.

CONCLUSIONS

These findings suggest that the organic and inorganic constituents present in CaOx stones are not structured as "brick and mortar" configurations in terms of inorganic and organic components.

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

Background

Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis.

Methods

Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions.

Results

Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 μm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite.

Conclusions

These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.

Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature

The Scleractinian corals Orbicella annularis and O. faveolata have survived by acclimatizing to environmental changes in water depth and sea surface temperature (SST). However, the complex physiological mechanisms by which this is achieved remain only partially understood, limiting the accurate prediction of coral response to future climate change. This study quantitatively tracks spatial and temporal changes in Symbiodiniaceae and biomolecule (chromatophores, calmodulin, carbonic anhydrase and mucus) abundance that are essential to the processes of acclimatization and biomineralization. Decalcified tissues from intact healthy Orbicella biopsies, collected across water depths and seasonal SST changes on Curaçao, were analyzed with novel autofluorescence and immunofluorescence histology techniques that included the use of custom antibodies. O. annularis at 5 m water depth exhibited decreased Symbiodiniaceae and increased chromatophore abundances, while O. faveolata at 12 m water depth exhibited inverse relationships. Analysis of seasonal acclimatization of the O. faveolata holobiont in this study, combined with previous reports, suggests that biomolecules are differentially modulated during transition from cooler to warmer SST. Warmer SST was also accompanied by decreased mucus production and decreased Symbiodiniaceae abundance, which is compensated by increased photosynthetic activity enhanced calcification. These interacting processes have facilitated the remarkable resiliency of the corals through geological time.

Demineralization and sectioning of human kidney stones: A molecular investigation revealing the spatial heterogeneity of the stone matrix

The molecular mechanisms by which kidney stones grow are largely unknown. Organic molecules from the urine combine with mineral crystals to form stones, but analysis of the stone matrix has revealed over a thousand different proteins, with no clues as to which are important for stone growth. Molecules that are present in every layer of a stone would be candidates for having an essential function, and thus the analysis of the stone matrix at a microscopic level is necessary. For this purpose, kidney stones were demineralized, sectioned, stained, and imaged by microscopy, using micro CT for precise orientation. Histological staining demonstrated heterogeneity in the density of adjacent layers within stones. Additional results also showed brilliant and unique autofluorescence patterns in decalcified nephroliths, indicating heterogeneous organic composition in adjacent layers. Regions of calcium oxalate (CaOx) stones were dissected using laser microdissection (LMD) for protein analysis. LMD of broad regions of demineralized CaOx stone sections yielded the same proteins as those found in different specimens of pulverized CaOx stones. These innovative methodologies will allow spatial mapping of protein composition within the heterogeneous stone matrix. Proteins that consistently coincide spatially with mineral deposition would be candidates for molecules essential for stone growth. This kind of analysis will be required to assess which of the thousand proteins in the stone matrix may be fundamental for stone growth.

Evaluation of the effect of Moringa peregrina bark on the crystal habit and size of calcium oxalate monohydrate crystals in different stages of crystallization using experimental and theoretical methods

Moringa peregrina bark extract is found to successfully retard the nucleation and aggregation of calcium oxalate monohydrate crystals and distort their shape, a mechanism for which is proposed using molecular modeling.

Multimodal imaging reveals a unique autofluorescence signature of Randall's plaque

Kidney stones frequently develop as an overgrowth on Randall's plaque (RP) which is formed in the papillary interstitium. The organic composition of RP is distinct from stone matrix in that RP contains fibrillar collagen; RP in tissue has also been shown to have two proteins that are also found in stones, but otherwise the molecular constituents of RP are unstudied. We hypothesized that RP contains unique organic molecules that can be differentiated from the stone overgrowth by fluorescence. To test this, we used micro-CT-guided polishing to expose the interior of kidney stones for multimodal imaging with multiphoton, confocal and infrared microscopy. We detected a blue autofluorescence signature unique to RP, the specificity of which was also confirmed in papillary tissue from patients with stone disease. High-resolution mineral mapping of the stone also showed a transition from the apatite within RP to the calcium oxalate in the overgrowth, demonstrating the molecular and spatial transition from the tissue to the urine. This work provides a systematic and practical approach to uncover specific fluorescence signatures which correlate with mineral type, verifies previous observations regarding mineral overgrowth onto RP and identifies a novel autofluorescence signature of RP demonstrating RP's unique molecular composition.

Assessing the Role of Light Absorption in Laser Lithotripsy by Isotopic Substitution of Kidney Stone Materials

Understanding the chemical characteristics of kidney stones and how the stone composition affects their fragmentation is key to improving clinical laser lithotripsy. During laser lithotripsy, two mechanisms may be responsible for stone fragmentation: a photothermal mechanism and/or microexplosion mechanism. Herein, we carry out an isotopic substitution of crystal H₂O with D₂O in calcium oxalate monohydrate and struvite stones to alter their optical properties to study the relationship between the absorption of the stones, at the wavelength of the Ho:YAG (2.12 μm) laser, and the fragmentation behavior. Changing the absorption of the stones at 2.12 μm changes the extent of fragmentation, whereas changing the absorption of the bulk medium has a negligible effect on fragmentation, leading to the conclusion that kidney stone ablation is dominated by a photothermal mechanism.

Hexametaphosphate as a potential therapy for the dissolution and prevention of kidney stones

The incidence of kidney stones is increasing worldwide, and recurrence is common (50% within 5 years). Citrate, the current gold standard therapy, which is usually given as potassium or sodium salts, is used because it raises urine pH and chelates calcium, the primary component of up to 94% of stones. In this study hexametaphosphate (HMP), a potent calcium chelator, was found to be 12 times more effective at dissolving calcium oxalate, the primary component of kidney stones, than citrate. HMP was also observed to be effective against other common kidney stone components, namely calcium phosphate and struvite (magnesium ammonium phosphate). Interestingly, HMP was capable of raising the zeta potential of calcium oxalate particles from -15.4 to -34.6 mV, which may prevent stone growth by aggregation, the most rapid growth mechanism, and thus avert occlusion. Notably, HMP was shown to be up to 16 times as effective as citrate at dissolving human kidney stones under simulated physiological conditions. It may thus be concluded that HMP is a promising potential therapy for calcium and struvite kidney stones.

SEM-EDX linear scanning: a new tool for morpho-compositional analysis of growth bands in urinary stones

The genesis and growth of calculi are imprinted in their structure, so the pathogenesis of lithiasis could potentially be read via proper analytical techniques. In this study, electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX) is used to obtain a description of the morphology and compositional structure of a single bladder stone. This technique establishes the chemical and crystalline architecture of the urolith to assess the effect of the chemical environment on its growth. Scanning electron microscopy-backscattered electrons (SEM-BSE) images clearly show that the stone has a multilayered structure. These layers and Liesegang ring-like structures are characterized by one predominant chemical component but also by slighter compositional changes. The mean crystalline components are determined by X-ray diffraction (DRX), infrared spectroscopy (FT-IR), and Raman analysis (RMN). Elemental analysis along a radial trajectory of the calculus by EDX linear scanning (EDX-LS) also reveals the compositional structure of the layers and the spatial distribution of the main chemical components. EDX-LS data processing reveals concentration profiles that clearly show morpho-compositional growth bands, which correspond to precipitation waves and urinary concentration peaks. The width of the growth bands is independent of the radial position, layer, and element analyzed. We conclude that the bands observed are a consequence of slight changes in the biochemical composition of the urine and consequently reflect a short-term biological cycle of the renal system. This non-specific growth rate suggests that stone formation is a kinetically controlled phenomenon in which promoters of crystal cluster aggregation may have played a key role.

The surgeon's role on chemical investigations of the composition of urinary stones

The chemical analysis of an urolith is often interpreted as "stone's composition". However, it must be taken into consideration, that in most cases, only a fragment of the stone has been sent to the laboratory. In some recurrent patients, stone compositions either vary considerably between episodes or the analytical result obtained from the stone fragment does not fit with the data of e.g. current 24 h-urinalysis or urinary pH-records. The question arises, whether this outcome may be the result of an improper stone sampling scheme. On a simple layered 2D-stone model composed of two mineral phases it is shown, how the choice of a stone fragment process may influence the result of "stone composition". Depending on the initial position of fragment within the whole stone, the respective calculated analyses can relevantly differ from the whole stone composition as well as strongly between two fragments. Even under the simplified conditions of a 2D-2-component-model "grown" under defined conditions, the differences between the analyses of the different specimens taken from a stone are in part remarkable. The more it can be argued that these differences increase if a real 3D-urolith is investigated. Further sampling biases may evolve and increase the problem of proper sampling:, e.g., if an urolith's more resistant parts remain intact while ESWL or laser-based stone fragmentation ("dusting"), the weak parts became fully disintegrated and removed from the body as fine-grained sludge-the stone's fine fraction is lost although its composition may carry important information on the stone's pathogenesis. Consequently, a "stone analysis" only obtained from the harder remains reveals an incomplete result, a fact that in principle limits its clinical interpretation. Choice of stone fragment is crucial. The extent of the uncertainty of an analysis resulting from potential selection biases should not be underestimated. Thus, sampling should be considered as an important part of the processes of quality assurance and management. Errors made at this early stage of diagnosis finding will affect the analytical result and thus influence the clarification of the underlying pathomechanism. This can lead to an improper metaphylactic strategy potentially causing recurrent stone formation which otherwise would have been prevented. A decision scheme for analysis of urinary stones removed using endoscopic methods is suggested.

Cooperative effects of Na+ and citrates on the dissolution of calcium oxalate crystals

Cooperative role of sodium and citrate ions in the dissolution of calcium oxalate crystals.

Polymer-Mineral Composites Mimic Human Kidney Stones in Laser Lithotripsy Experiments

Despite the widespread use of laser lithotripsy to fragment kidney stones in vivo, there is a lack of robust artificial stone models to replicate the behavior of human stones during lithotripsy procedures. This need for accurate stone models is particularly important as novel laser technologies are introduced in the field of lithotripsy. In this work, we present a method to prepare composite materials that replicate the properties of human kidney stones during laser lithotripsy. Their behavior is understood through the lens of near-IR spectroscopy and helps to elucidate the mechanism of laser lithotripsy in kidney stone materials.

A Confocal Reflection Super-Resolution Technique to Image Golgi-Cox Stained Neurons

Metal-based Golgi-Cox (GC) staining is an established method used to visualise neurons with great morphological detail. Although GC stained samples are imaged routinely under transmitted light microscopy, this method is unable to yield information on the three-dimensional structure of dendrites and neurons and thus help reveal the connective properties of the central nervous system. Although a few studies have attempted simultaneous visualisation of GC staining and antigen-specific fluorescent labelling under a confocal reflection technique, the resolution of both confocal reflection and fluorescence modalities used to acquire GC reflection and fluorescently stained antibody signals are still limited by the diffraction limit of light at about 220 nm. Here, we report a confocal reflection super-resolution technique (CRSR) to break this diffraction barrier, which is achieved by minimising the pinhole size from 1 airy unit (AU) to 0.1 AU. This is achieved by minimising or closing the confocal pinhole size and is possible in this reflection modality, unlike fluorescence, because it is not a photon limited technique. Utilising the lowest wavelength of light available in the system (405 nm), the CRSR technique results in ∼30% lateral and axial resolution improvement. We also show that the CRSR technique can be used in conjunction to visualise both GC and immunofluorescence targets to create precise and improved three-dimensional visualisation and analysis. In addition, using these superresolution confocal reflection data sets from GC in CRSR mode significantly reduced the data overestimation, improving the accuracy of statistical analysis of dendritic spine density and average spine dimensions. Combining the 0.1 AU setting with deconvolution routines, the signal-to-noise ratio and resolution could further be improved an additional ∼20-25%, yielding CRSR images with resolutions up to 2-fold over the diffraction limit both laterally and axially. The improved precision of both visualisation and quantification of subdiffraction limited dendritic spines using the CRSR technique may prove to be critical in investigations that concern changes in detailed neuron morphology under central nervous system disease conditions such as multiple sclerosis and Alzheimer's disease. LAY DESCRIPTION: For over a century, Golgi-Cox (GC) has been a leading staining technique in the field of neuroscience, used to visualise neurons with great morphological detail. GC stained brain or spinal cord samples are conventionally visualised under transmitted light techniques. This limits the view of Golgi-staining to a two-dimensional image. A recent report showed that Golgi staining can be visualised in three-dimensions using the reflection modality of the confocal microscope. This visualisation also allows for the simultaneous acquisition of immunofluorescence signals. However, the reported resolution of Golgi staining confocal reflection is limited by the diffraction limit of light, which is around 220 nm. Here, we report a superresolution confocal reflection technique (CRSR) that achieves superresolution by minimising the pinhole size used in confocal microscopy. The CRSR technique results in ∼30% lateral and axial resolution improvement. Adding a deconvolution step in the final processing could improve the SNR and resolution even further up to 2-fold improvement in resolution over the diffraction limit both laterally and axially. We hope that this improved visualisation will help in investigations that concern changes in detailed neuron morphology under central nervous system disease conditions such as multiple sclerosis and Alzheimer's disease.

Morphological characteristics and microstructure of kidney stones using synchrotron radiation μCT reveal the mechanism of crystal growth and aggregation in mixed stones

Understanding the mechanisms of kidney stone formation, development patterns and associated pathological features are gaining importance due to an increase in the prevalence of the disease and diversity in the presentation of the stone composition. Based on the microstructural characteristics of kidney stones, it may be possible to explain the differences in the pathogenesis of pure and mixed types of stones. In this study, the microstructure and distribution of mineral components of kidney stones of different mineralogy (pure and mixed types) were analyzed. The intact stones removed from patients were investigated using synchrotron radiation X-ray computed microtomography (SR-μCT) and the tomography slice images were reconstructed representing the density and structure distribution at various elevation planes. Infrared (IR) spectroscopes, X-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to confirm the bulk mineral composition in the thin section stones. Observations revealed differences in the micro-morphology of the kidney stones with similar composition in the internal 3-D structure. Calcium oxalate monohydrate stones showed well-organised layering patterns, while uric acid stones showed lower absorption signals with homogenous inner structure. Distinct mineral phases in the mixed types were identified based on the differential absorption rates. The 3-D quantitative analysis of internal porosity and spatial variation between nine different types of stones were compared. The diversity among the microstructure of similar and different types of stones shows that the stone formation is complex and may be governed by both physiological and micro-environmental factors. These factors may predispose a few towards crystal aggregation and stone growth, while, in others the crystals may not establish stable attachment and/or growth.