GeoBioMed sheds new light on human kidney stone crystallization and dissolution

Ambra1 in exosomes secreted by HK-2 cells damaged by supersaturated oxalate induce mitophagy and autophagy-ferroptosis in normal HK-2 cells to participate in the occurrence of kidney stones

Injury to the renal tubular epithelium has emerged as a leading factor underlying the formation of kidney stones. Indeed, epithelial cell damage contributes to the adherence and aggregation of crystals, thereby accelerating the formation of renal stones. Meanwhile, exosomes play an instrumental role in cellular communication, including DNA, RNA, mRNA, etc. In this study, homogenous cells were treated with exosomes derived from damaged cells in an attempt to establish "positive feedback" of cell damage, and the desired results were achieved. To begin, a serum-free medium and supersaturated concentrations of oxalate were added to the HK-2 cell line, and then exosomes were isolated from the two groups for analysis and comparison, and the autophagy-related gene Ambra1 (autophagy and beclin-1 regulator 1) was detected. Subsequently, normal HK-2 cells were treated with exosomes, and the related indexes of autophagy, ferroptosis and mitophagy were determined. Thereafter, Ambra1 was knocked down in exosome-derived HK-2 cells, resulting in the down-regulation of Ambra1 expression in exosomes produced by HK-2 cells following oxalate intervention. Thereafter, the ability of exosomes to stimulate autophagy, mitophagy and ferroptosis was re-evaluated in HK-2 cells after Ambra1 knockdown. The results corroborated that exosomes secreted by oxalate-treated HK-2 can directly elevate autophagy, ferroptosis and mitophagy levels in normal cells, and this effect was significantly mitigated following Ambra1 knockdown within exosomes. Meanwhile, exosomes-induced autophagy and ferroptosis were alleviated after knockdown of beclin-1 in recipient HK-2 cells. These results further suggest that beclin-1 plays a critical role in the process of exosome-induced autophagy-ferroptosis.

Performance of brushite plaster as kidney stone phantoms for laser lithotripsy

Artificial phantoms used in photothermal near-infrared laser lithotripsy research generally fail to mimic both the chemical and the physical properties of human stones. Though high-energy, 1 J pulses are capable of fracturing hard human stones into several large fragments along natural boundaries, similar behavior has not been observed in commonly used gypsum plasters like BegoStone. We developed a new brushite-based plaster formulation composed of ≈90% brushite that undergoes rapid fracture in the manner of human stones under fragmentation pulse regimes. Single-pulse (1 J) ablation crater volumes for phantoms were not significantly different from those of pure brushite stones. Control over crater volumes was demonstrated by varying phosphorous acid concentration in the plaster formulation. Fragmentation of cylindrical brushite phantoms was filmed using a high-speed camera which demonstrated rapid fragmentation in < 100 µs during the bubble expansion phase of a short pulse from a high-powered Ho:YAG laser (Lumenis Pulse 120 H). The rapid nature of observed fracture suggests increasing laser pulse energy by increasing laser pulse duration will not improve fragmentation performance of laser lithotripters. Brushite plaster phantoms are a superior alternative to gypsum plasters for laser lithotripsy research due to their better mimicry of stone composition, controllable single-pulse crater volumes, and fragmentation behavior.

Detection of Cadmium and Lead in Kidney Stones. Associations with Patient Demographics, Stone Composition, and Smoking

BACKGROUND

Kidney stones are a highly prevalent disease worldwide. Additionally, both environmental and occupational exposure to Pb and Cd continue to be prevalent globally and can result in renal toxicity. The objective of this study was to examine the potential presence of Pb and Cd in kidney stones, and to assess for correlation with demographic factors including smoking, gender, age, and kidney stone matrix composition.

METHODS

Patient kidney stones (n = 96) were analyzed using Fourier transform infrared spectroscopy to identify the stone constituents. Cd and Pb concentrations (µg/g) were determined by inductively coupled plasma mass spectrometry. Cd and Pb concentrations were correlated using bivariable and multivariable statistical analysis with demographic factors (age, gender, smoking status), and kidney stone composition.

RESULTS

Kidney stone Cd (median 0.092 µg/g, range 0.014 to 2.46) and Pb concentrations (median 0.95 µg/g, range 0.060 to 15.4) were moderately correlated (r = 0.56, P < 0.0001). Cd concentrations were positively associated with patient history of smoking, patient age, and calcium oxalate monohydrate levels while negatively associated with struvite and uric acid/uric acid dihydrate. Pb concentrations were positively associated with females and apatite levels while negatively associated with uric acid/uric acid dihydrate. After holding constant other stone type composition levels, smoking status, and age, both Pb and Cd were positively associated with apatite and negatively associated with uric acid/uric acid dihydrate, struvite, and calcium carbonate.

CONCLUSIONS

Cd and Pb kidney stone concentrations are associated with specific kidney stone types. Cd and Pb kidney stone concentrations are both associated with smoking.

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.

Assessment of gadolinium and iodine concentrations in kidney stones and correlation with contrast agent exposure, stone matrix composition, and patient demographic factors

BACKGROUND

Gadolinium-based contrast agents (GBCAs) and Iodinated contrast media are widely utilized to increase medical imaging sensitivity. With predominant renal elimination, the potential for the incorporation of contrast agent derived gadolinium and iodine into kidney stones remains largely uncharacterized. The study objective was to measure gadolinium and iodine concentrations within kidney stones. Observed elemental concentrations were correlated with prior contrast agent administration, kidney stone composition, age, gender, and smoking status.

METHODS

Kidney stones from 96 patients were analyzed by Fourier Transform Infrared Spectroscopy to determine stone composition. Residual kidney stone material was digested and analyzed by Inductively Coupled Plasma Mass Spectrometry to determine gadolinium and iodine concentrations. Univariable and multivariable lognormal linear regression were performed to study the relationship between kidney stone element concentrations and contrast agent administration, kidney stone composition, age, gender, and smoking status.

RESULTS

Median iodine and gadolinium stone concentrations were 6.4 (range 0.6-3997) and 0.1 (range ≤0.013-113.5) µg/g respectively. Elevated gadolinium was strongly associated with GBCA history with a hazard rate of 2.20 (95 % CI 1.14-3.25 P < 0.001). Gadolinium was positively associated with smoking, as well as stones comprised of apatite and calcium oxalate. Iodine concentrations were negatively associated with uric acid stones.

CONCLUSION

Gadolinium, but not iodine, concentrations in kidney stones was strongly correlated with contrast exposure history. Stone matrix composition and demographic factors, particularly smoking, can influence observed kidney stone elemental concentrations. Additional studies are needed to determine if exposure to gadolinium and iodine promote the formation of stone matrix and/or reflect exposure history.

The COVID-19-diabetes mellitus molecular tetrahedron

Accumulating molecular evidence suggests that insulin resistance, rather than SARS-CoV-2- provoked beta-cell impairment, plays a major role in the observed rapid metabolic deterioration in diabetes, or new-onset hyperglycemia, during the COVID-19 clinical course. In order to clarify the underlying complexity of COVID-19 and diabetes mellitus interactions, we propose the imaginary diabetes-COVID-19 molecular tetrahedron with four lateral faces consisting of SARS-CoV-2 entry via ACE2 (lateral face 1), the viral hijacking and replication (lateral face 2), acute inflammatory responses (lateral face 3), and the resulting insulin resistance (lateral face 4). The entrance of SARS-CoV-2 using ACE2 receptor triggers an array of multiple molecular signaling beyond that of the angiotensin II/ACE2-Ang-(1-7) axis, such as down-regulation of PGC-1 α/irisin, increased SREBP-1c activity, upregulation of CD36 and Sirt1 inhibition leading to insulin resistance. In another arm of the molecular cascade, the SARS-CoV-2 hijacking and replication induces a series of molecular events in the host cell metabolic machinery, including upregulation of SREBP-2, decrement in Sirt1 expression, dysregulation in PPAR-ɣ, and LPI resulting in insulin resistance. The COVID-19-diabetes molecular tetrahedron may suggest novel targets for therapeutic interventions to overcome insulin resistance that underlies the pathophysiology of worsening metabolic control in patients with diabetes mellitus or the new-onset of hyperglycemia in COVID-19.

Deciphering the link between Diabetes mellitus and SARS-CoV-2 infection through differential targeting of microRNAs in the human pancreas

PURPOSE

Coronavirus Disease 2019 (COVID-19) severity and Diabetes mellitus affect each other bidirectionally. However, the cause of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection on the incidence of diabetes is unclear. In the SARS-CoV-2-infected cells, host microRNAs (miRNAs) may target the native gene transcripts as well as the viral genomic and subgenomic RNAs. Here, we investigated the role of miRNAs in linking Diabetes to SARS-CoV-2 infection in the human pancreas.

METHODS

Differential gene expression and disease enrichment analyses were performed on an RNA-Seq dataset of human embryonic stem cell-derived (hESC) mock-infected and SARS-CoV-2-infected pancreatic organoids to obtain the dysregulated Diabetes-associated genes. The miRNA target prediction for the Diabetes-associated gene transcripts and the SARS-CoV-2 RNAs has been made to determine the common miRNAs targeting them. Minimum Free Energy (MFE) analysis was done to identify the miRNAs, preferably targeting SARS-CoV-2 RNAs over the Diabetes-associated gene transcripts.

RESULTS

The gene expression and disease enrichment analyses of the RNA-Seq data have revealed five biomarker genes, i.e., CP, SOCS3, AGT, PSMB8 and CFB that are associated with Diabetes and get significantly upregulated in the pancreas following SARS-CoV-2-infection. Four miRNAs, i.e., hsa-miR-298, hsa-miR-3925-5p, hsa-miR-4691-3p and hsa-miR-5196-5p, showed preferential targeting of the SARS-CoV-2 genome over the cell's Diabetes-associated messenger RNAs (mRNAs) in the human pancreas.

CONCLUSION

Our study proposes that the differential targeting of the Diabetes-associated host genes by the miRNAs may lead to diabetic complications or new-onset Diabetes that can worsen the condition of COVID-19 patients.

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.

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.

What Justifies the Allocation of Health Care Resources to Patients with Disorders of Consciousness?

This paper critically engages ethical issues in the allocation of novel, and potentially costly, health care resources to patients with disorders of consciousness. First, we review potential benefits of novel health care resources for patients and their families and outline preliminary considerations to address concerns about cost. We then address two problems regarding the allocation of health care resources to patients with disorders of consciousness: (1) the problem of uncertain moral status; and (2) the problem of accurately measuring the welfare burdens these resources would relieve. We conclude by suggesting that opportunity-based frameworks might complement standard approaches for justifying resources allocation to patients with disorders of consciousness.

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.