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1.
Biomolecules ; 14(5)2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38785918

ABSTRACT

Primary hyperoxalurias (PHs) are inherited metabolic disorders marked by enzymatic cascade disruption, leading to excessive oxalate production that is subsequently excreted in the urine. Calcium oxalate deposition in the renal tubules and interstitium triggers renal injury, precipitating systemic oxalate build-up and subsequent secondary organ impairment. Recent explorations of novel therapeutic strategies have challenged and necessitated the reassessment of established management frameworks. The execution of diverse clinical trials across various medication classes has provided new insights and knowledge. With the evolution of PH treatments reaching a new milestone, prompt and accurate diagnosis is increasingly critical. Developing early, effective management and treatment plans is essential to improve the long-term quality of life for PH patients.


Subject(s)
Hyperoxaluria, Primary , Humans , Hyperoxaluria, Primary/drug therapy , Hyperoxaluria, Primary/therapy , Calcium Oxalate/metabolism , Oxalates/metabolism , Quality of Life
2.
J Agric Food Chem ; 72(18): 10163-10178, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38653191

ABSTRACT

Oxalate decarboxylase (OXDC) is a typical Mn2+/Mn3+ dependent metal enzyme and splits oxalate to formate and CO2 without any organic cofactors. Fungi and bacteria are the main organisms expressing the OXDC gene, but with a significantly different mechanism of gene expression and regulation. Many articles reported its potential applications in the clinical treatment of hyperoxaluria, low-oxalate food processing, degradation of oxalate salt deposits, oxalate acid diagnostics, biocontrol, biodemulsifier, and electrochemical oxidation. However, some questions still remain to be clarified about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II)/Mn(III), the nature of dioxygen involved in the catalytic mechanism, and how OXDC acquires Mn(II) /Mn(III). This review mainly summarizes its biochemical and structure characteristics, gene expression and regulation, and catalysis mechanism. We also deep-mined oxalate decarboxylase gene data from National Center for Biotechnology Information to give some insights to explore new OXDC with diverse biochemical properties.


Subject(s)
Bacteria , Carboxy-Lyases , Carboxy-Lyases/genetics , Carboxy-Lyases/metabolism , Carboxy-Lyases/chemistry , Bacteria/genetics , Bacteria/enzymology , Bacteria/metabolism , Fungi/genetics , Fungi/enzymology , Fungal Proteins/genetics , Fungal Proteins/metabolism , Fungal Proteins/chemistry , Biocatalysis , Oxalates/metabolism , Oxalates/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Gene Expression Regulation, Enzymologic , Humans , Catalysis , Animals
3.
Curr Opin Nephrol Hypertens ; 33(4): 398-404, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38602143

ABSTRACT

PURPOSE OF REVIEW: Primary hyperoxalurias (PHs) are rare disorders caused by the deficit of liver enzymes involved in glyoxylate metabolism. Their main hallmark is the increased excretion of oxalate leading to the deposition of calcium oxalate stones in the urinary tract. This review describes the molecular aspects of PHs and their relevance for the clinical management of patients. RECENT FINDINGS: Recently, the study of PHs pathogenesis has received great attention. The development of novel in vitro and in vivo models has allowed to elucidate how inherited mutations lead to enzyme deficit, as well as to confirm the pathogenicity of newly-identified mutations. In addition, a better knowledge of the metabolic consequences in disorders of liver glyoxylate detoxification has been crucial to identify the key players in liver oxalate production, thus leading to the identification and validation of new drug targets. SUMMARY: The research on PHs at basic, translational and clinical level has improved our knowledge on the critical factors that modulate disease severity and the response to the available treatments, leading to the development of new drugs, either in preclinical stage or, very recently, approved for patient treatment.


Subject(s)
Hyperoxaluria, Primary , Mutation , Humans , Hyperoxaluria, Primary/genetics , Hyperoxaluria, Primary/therapy , Hyperoxaluria, Primary/metabolism , Animals , Liver/metabolism , Liver/pathology , Glyoxylates/metabolism , Genetic Predisposition to Disease , Phenotype , Oxalates/metabolism
4.
World J Microbiol Biotechnol ; 40(6): 178, 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38662173

ABSTRACT

Oxalic acid and oxalates are secondary metabolites secreted to the surrounding environment by fungi, bacteria, and plants. Oxalates are linked to a variety of processes in soil, e.g. nutrient availability, weathering of minerals, or precipitation of metal oxalates. Oxalates are also mentioned among low-molecular weight compounds involved indirectly in the degradation of the lignocellulose complex by fungi, which are considered to be the most effective degraders of wood. The active regulation of the oxalic acid concentration is linked with enzymatic activities; hence, the biochemistry of microbial biosynthesis and degradation of oxalic acid has also been presented. The potential of microorganisms for oxalotrophy and the ability of microbial enzymes to degrade oxalates are important factors that can be used in the prevention of kidney stone, as a diagnostic tool for determination of oxalic acid content, as an antifungal factor against plant pathogenic fungi, or even in efforts to improve the quality of edible plants. The potential role of fungi and their interaction with bacteria in the oxalate-carbonate pathway are regarded as an effective way for the transfer of atmospheric carbon dioxide into calcium carbonate as a carbon reservoir.


Subject(s)
Bacteria , Biotechnology , Fungi , Oxalic Acid , Oxalic Acid/metabolism , Fungi/metabolism , Bacteria/metabolism , Biotechnology/methods , Plants/microbiology , Plants/metabolism , Oxalates/metabolism , Lignin/metabolism
5.
Ren Fail ; 46(1): 2334396, 2024 Dec.
Article in English | MEDLINE | ID: mdl-38570195

ABSTRACT

OBJECTIVES: Calcium oxalate (CaOx) crystal deposition in acute kidney injury (AKI) patients is under recognized but impacts renal outcomes. This study investigates its determinants and effects. METHODS: We studied 814 AKI patients with native kidney biopsies from 2011 to 2020, identifying CaOx crystal deposition severity (mild: <5, moderate: 5-10, severe: >10 crystals per section). We assessed factors like urinary oxalate, citrate, urate, electrolytes, pH, tubular calcification index, and SLC26A6 expression, comparing them with creatinine-matched AKI controls without oxalosis. We analyzed how these factors relate to CaOx severity and their impact on renal recovery (eGFR < 15 mL/min/1.73 m2 at 3-month follow-up). RESULTS: CaOx crystal deposition was found in 3.9% of the AKI cohort (32 cases), with 72% due to nephrotoxic medication-induced tubulointerstitial nephritis. Diuretic use, higher urinary oxalate-to-citrate ratio induced by hypocitraturia, and tubular calcification index were significant contributors to moderate and/or severe CaOx deposition. Poor baseline renal function, low urinary chloride, high uric acid and urea nitrogen, tubular SLC26A6 overexpression, and glomerular sclerosis were also associated with moderate-to-severe CaOx deposition. Kidney recovery was delayed, with 43.8%, 31.2%, and 18.8% of patients having eGFR < 15 mL/min/1.73 m2 at 4, 12, and 24-week post-injury. Poor outcomes were linked to high urinary α1-microglobulin-to-creatinine (α1-MG/C) ratios and active tubular injury scores. Univariate analysis showed a strong link between this ratio and poor renal outcomes, independent of oxalosis severity. CONCLUSIONS: In AKI, CaOx deposition is common despite declining GFR. Factors worsening tubular injury, not just oxalate-to-citrate ratios, are key to understanding impaired renal recovery.


Subject(s)
Acute Kidney Injury , Calcinosis , Hyperoxaluria , Humans , Calcium Oxalate/chemistry , Creatinine/metabolism , Kidney/pathology , Hyperoxaluria/complications , Oxalates/metabolism , Acute Kidney Injury/pathology , Citrates/metabolism , Citric Acid
6.
Comput Biol Chem ; 110: 108039, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38471352

ABSTRACT

Hepatocellular carcinoma (HCC) persists to be one of the most devastating and deadliest malignancies globally. Recent research into the molecular signaling networks entailed in many malignancies has given some prominent insights that can be leveraged to create molecular therapeutics for combating HCC. Therefore, in the current communication, an in-silico drug repurposing approach has been employed to target the function of PTP4A3/PRL-3 protein in HCC using antidepressants: Fluoxetine hydrochloride, Citalopram, Amitriptyline, Imipramine, and Escitalopram oxalate as the desired ligands. The density function theory (DFT) and chemical absorption, distribution, metabolism, excretion, and toxicity (ADMET) parameters for the chosen ligands were evaluated to comprehend the pharmacokinetics, drug-likeness properties, and bioreactivity of the ligands. The precise interaction mechanism was explored using computational methods such as molecular docking and molecular dynamics (MD) simulation studies to assess the inhibitory effect and the stability of the interactions against the protein of interest. Escitalopram oxalate exhibited a comparatively significant docking score (-7.4 kcal/mol) compared to the control JMS-053 (-6.8 kcal/mol) against the PRL-3 protein. The 2D interaction plots exhibited an array of hydrophobic and hydrogen bond interactions. The findings of the ADMET forecast confirmed that it adheres to Lipinski's rule of five with no violations, and DFT analysis revealed a HOMO-LUMO energy gap of -0.26778 ev, demonstrating better reactivity than the control molecule. The docked complexes were subjected to MD studies (100 ns) showing stable interactions. Considering all the findings, it can be concluded that Escitalopram oxalate and related therapeutics can act as potential pharmacological candidates for targeting the activity of PTP4A3/PRL-3 in HCC.


Subject(s)
Antidepressive Agents , Carcinoma, Hepatocellular , Escitalopram , Liver Neoplasms , Molecular Docking Simulation , Protein Tyrosine Phosphatases , Humans , Liver Neoplasms/drug therapy , Liver Neoplasms/metabolism , Carcinoma, Hepatocellular/drug therapy , Carcinoma, Hepatocellular/metabolism , Protein Tyrosine Phosphatases/antagonists & inhibitors , Protein Tyrosine Phosphatases/metabolism , Antidepressive Agents/pharmacology , Antidepressive Agents/chemistry , Escitalopram/chemistry , Escitalopram/pharmacology , Neoplasm Proteins/metabolism , Neoplasm Proteins/antagonists & inhibitors , Molecular Dynamics Simulation , Oxalates/chemistry , Oxalates/metabolism , Density Functional Theory , Molecular Structure , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry
7.
J Agric Food Chem ; 72(12): 6372-6388, 2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38471112

ABSTRACT

Oxidative damage to the kidneys is a primary factor in the occurrence of kidney stones. This study explores the inhibitory effect of Porphyra yezoensis polysaccharides (PYP) on oxalate-induced renal injury by detecting levels of oxidative damage, expression of adhesion molecules, and damage to intracellular organelles and revealed the molecular mechanism by molecular biology methods. Additionally, we validated the role of PYP in vivo using a crystallization model of hyperoxalate-induced rats. PYP effectively scavenged the overproduction of reactive oxygen species (ROS) in HK-2 cells, inhibited the adhesion of calcium oxalate (CaOx) crystals on the cell surface, unblocked the cell cycle, restored the depolarization of the mitochondrial membrane potential, and inhibited cell death. PYP upregulated the expression of antioxidant proteins, including Nrf2, HO-1, SOD, and CAT, while decreasing the expression of Keap-1, thereby activating the Keap1/Nrf2 signaling pathway. PYP inhibited CaOx deposition in renal tubules in the rat crystallization model, significantly reduced high oxalate-induced renal injury, decreased the levels of the cell surface adhesion proteins, improved renal function in rats, and ultimately inhibited the formation of kidney stones. Therefore, PYP, which has crystallization inhibition and antioxidant properties, may be a therapeutic option for the treatment of kidney stones.


Subject(s)
Calcium Oxalate , Edible Seaweeds , Kidney Calculi , Porphyra , Rats , Animals , Kelch-Like ECH-Associated Protein 1/metabolism , Calcium Oxalate/metabolism , Calcium Oxalate/pharmacology , Antioxidants/metabolism , NF-E2-Related Factor 2/metabolism , Kidney/metabolism , Kidney Calculi/metabolism , Oxidative Stress , Oxalates/metabolism , Oxalates/pharmacology , Polysaccharides/metabolism
8.
Urolithiasis ; 52(1): 46, 2024 Mar 23.
Article in English | MEDLINE | ID: mdl-38520518

ABSTRACT

This study was aimed to investigate the preventive effects of N-acetyl-L-cysteine (NAC) against renal tubular cell injury induced by oxalate and stone formation and further explore the related mechanism. Transcriptome sequencing combined with bioinformatics analysis were performed to identify differentially expressed gene (DEG) and related pathways. HK-2 cells were pretreated with or without antioxidant NAC/with or silencing DEG before exposed to sodium oxalate. Then, the cell viability, oxidative biomarkers of superoxidase dismutase (SOD) and malondialdehyde (MDA), apoptosis and cell cycle were measured through CCK8, ELISA and flow cytometry assay, respectively. Male SD rats were separated into control group, hyperoxaluria (HOx) group, NAC intervention group, and TGF-ß/SMAD pathway inhibitor group. After treatment, the structure changes and oxidative stress and CaOx crystals deposition were evaluated in renal tissues by H&E staining, immunohistochemical and Pizzolato method. The expression of TGF-ß/SMAD pathway related proteins (TGF-ß1, SMAD3 and SMAD7) were determined by Western blot in vivo and in vitro. CDKN2B is a DEG screened by transcriptome sequencing combined with bioinformatics analysis, and verified by qRT-PCR. Sodium oxalate induced declined HK-2 cell viability, in parallel with inhibited cellular oxidative stress and apoptosis. The changes induced by oxalate in HK-2 cells were significantly reversed by NAC treatment or the silencing of CDKN2B. The cell structure damage and CaOx crystals deposition were observed in kidney tissues of HOx group. Meanwhile, the expression levels of SOD and 8-OHdG were detected in kidney tissues of HOx group. The changes induced by oxalate in kidney tissues were significantly reversed by NAC treatment. Besides, expression of SMAD7 was significantly down-regulated, while TGF-ß1 and SMAD3 were accumulated induced by oxalate in vitro and in vivo. The expression levels of TGF-ß/SMAD pathway related proteins induced by oxalate were reversed by NAC. In conclusion, we found that NAC could play an anti-calculus role by mediating CDKN2B/TGF-ß/SMAD axis.


Subject(s)
Hyperoxaluria , Oxalates , Animals , Male , Rats , Acetylcysteine/pharmacology , Calcium Oxalate/metabolism , Epithelial Cells/metabolism , Hyperoxaluria/chemically induced , Hyperoxaluria/metabolism , Oxalates/metabolism , Rats, Sprague-Dawley , Superoxide Dismutase/metabolism , Transforming Growth Factor beta1/metabolism
9.
Plant Physiol Biochem ; 208: 108475, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38430786

ABSTRACT

Saline-alkali stress significantly affects the growth and yield of alfalfa (Medicago sativa L.). Organic acid secretion is crucial in alleviating abiotic stress-induced damage in plants. In this study, we evaluated the contents of the major organic acids secreted by the roots of tolerant (ZD) and sensitive (LYL) varieties of alfalfa under saline-alkali stress and investigated the effects of these organic acids on the growth, and physiological functions of alfalfa. Our results indicated that the oxalic acid (OA) content was the highest among the organic acids secreted from alfalfa roots under saline-alkali stress, and oxalic acid content was the most significantly different between the two varieties, ZD and LYL, compared to the contents of the other organic acids. Oxalic acid alleviated the inhibition of alfalfa growth caused by saline-alkali stress, improved photosynthetic characteristics, reduced the accumulation of reactive oxygen species, and increased the activity of antioxidant enzymes and content of osmoregulatory substances. Furthermore, oxalic acid resulted in significantly increased expression of genes involved in photosynthesis and antioxidant system in alfalfa under saline-alkali stress. This study revealed the effects of oxalic acid secreted by the root system on stress-related physiological processes, providing valuable insights into the functions of root secretions in plant saline-alkali resistance.


Subject(s)
Antioxidants , Medicago sativa , Antioxidants/metabolism , Medicago sativa/genetics , Alkalies/metabolism , Photosynthesis , Oxalates/metabolism , Oxalates/pharmacology
10.
Clin Res Hepatol Gastroenterol ; 48(5): 102322, 2024 May.
Article in English | MEDLINE | ID: mdl-38503362

ABSTRACT

Enteric hyperoxaluria is a metabolic disorder resulting from conditions associated with fatty acid malabsorption and characterized by an increased urinary output of oxalate. Oxalate is excessively absorbed in the gut and then excreted in urine where it forms calcium oxalate crystals, inducing kidney stones formation and crystalline nephropathies. Enteric hyperoxaluria is probably underdiagnosed and may silently damage kidney function of patients affected by bowel diseases. Moreover, the prevalence of enteric hyperoxaluria has increased because of the development of bariatric surgical procedures. Therapeutic options are based on the treatment of the underlying disease, limitation of oxalate intakes, increase in calcium salts intakes but also increase in urine volume and correction of hypocitraturia. There are few data regarding the natural evolution of kidney stone events and chronic kidney disease in these patients, and there is a need for new treatments limiting kidney injury by calcium oxalate crystallization.


Subject(s)
Hyperoxaluria , Humans , Hyperoxaluria/therapy , Hyperoxaluria/complications , Hyperoxaluria/etiology , Oxalates/metabolism , Calcium Oxalate/metabolism , Malabsorption Syndromes/therapy , Malabsorption Syndromes/physiopathology , Malabsorption Syndromes/complications , Malabsorption Syndromes/etiology
11.
Int J Biol Macromol ; 261(Pt 2): 129912, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38309384

ABSTRACT

Stone modulators are various kinds of molecules that play crucial roles in promoting/inhibiting kidney stone formation. Several recent studies have extensively characterized the stone modulatory proteins with the ultimate goal of preventing kidney stone formation. Herein, we introduce the StoneMod 2.0 database (https://www.stonemod.org), which has been dramatically improved from the previous version by expanding the number of the modulatory proteins in the list (from 32 in the initial version to 17,130 in this updated version). The stone modulatory proteins were recruited from solid experimental evidence (via PubMed) and/or predicted evidence (via UniProtKB, QuickGO, ProRule, STITCH and OxaBIND to retrieve calcium-binding and oxalate-binding proteins). Additionally, StoneMod 2.0 has implemented a scoring system that can be used to determine the likelihood and to classify the potential stone modulatory proteins as either "solid" (modulator score ≥ 50) or "weak" (modulator score < 50) modulators. Furthermore, the updated version has been designed with more user-friendly interfaces and advanced visualization tools. In addition to the monthly scheduled update, the users can directly submit their experimental evidence online anytime. Therefore, StoneMod 2.0 is a powerful database with prediction scores that will be very useful for many future studies on the stone modulatory proteins.


Subject(s)
Calcium Oxalate , Kidney Calculi , Humans , Calcium Oxalate/chemistry , Kidney Calculi/chemistry , Proteins/metabolism , Carrier Proteins/metabolism , Oxalates/metabolism , Kidney/metabolism
12.
Microbiol Res ; 282: 127663, 2024 May.
Article in English | MEDLINE | ID: mdl-38422861

ABSTRACT

Formation of calcium oxalate (CaOx) crystal, the most common composition in kidney stones, occurs following supersaturation of calcium and oxalate ions in the urine. In addition to endogenous source, another main source of calcium and oxalate ions is dietary intake. In the intestinal lumen, calcium can bind with oxalate to form precipitates to be eliminated with feces. High intake of oxalate-rich foods, inappropriate amount of daily calcium intake, defective intestinal transporters for oxalate secretion and absorption, and gastrointestinal (GI) malabsorption (i.e., from gastric bypass surgery) can enhance intestinal oxalate absorption, thereby increasing urinary oxalate level and risk of kidney stone disease (KSD). The GI microbiome rich with oxalate-degrading bacteria can reduce intestinal oxalate absorption and urinary oxalate level. In addition to the oxalate-degrading ability, the GI microbiome also affects expression of oxalate transporters and net intestinal oxalate transport, cholesterol level, and short-chain fatty acids (SCFAs) production, leading to lower KSD risk. Recent evidence also shows beneficial effects of urinary microbiome in KSD prevention. This review summarizes the current knowledge on the aforementioned aspects. Potential benefits of the GI and urinary microbiomes as probiotics for KSD prevention are emphasized. Finally, challenges and future perspectives of probiotic treatment in KSD are discussed.


Subject(s)
Kidney Calculi , Microbiota , Humans , Oxalates/metabolism , Calcium/urine , Kidney Calculi/prevention & control , Kidney Calculi/urine , Calcium Oxalate/metabolism , Ions
13.
Urolithiasis ; 52(1): 38, 2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38413462

ABSTRACT

Intestinal microbiome dysbiosis is a known risk factor for recurrent kidney stone disease (KSD) with prior data suggesting a role for dysfunctional metabolic pathways other than those directly utilizing oxalate. To identify alternative mechanisms, the current study analyzed differences in the metabolic potential of intestinal microbiomes of patients (n = 17) and live-in controls (n = 17) and determined their relevance to increased risk for KSD using shotgun metagenomic sequencing. We found no differences in the abundance of genes associated with known oxalate degradation pathways, supporting the notion that dysfunction in other metabolic pathways plays a role in KSD. Further analysis showed decreased abundance of key enzymes involved in butyrate biosynthesis in patient intestinal microbiomes. Furthermore, de novo construction of microbial genomes showed that the majority of genes significantly enriched in non-stone formers are affiliated with Faecalibacterium prausnitzii, a major butyrate producer. Specifically pertaining to butyrate metabolism, the majority of abundant genes mapped back to F. prausnitzii, Alistipes spp., and Akkermansia muciniphila. No differences were observed in ascorbate or glyoxylate metabolic pathways. Collectively, these data suggest that impaired bacterial-associated butyrate metabolism may be an oxalate-independent mechanism that contributes to an increased risk for recurrent KSD. This indicates that the role of the intestinal microbiome in recurrent KSD is multi-factorial, which is representative of the highly intertwined metabolic nature of this complex environment. Future bacteria-based treatments must not be restricted to targeting only oxalate metabolism.


Subject(s)
Gastrointestinal Microbiome , Kidney Calculi , Humans , Oxalates/metabolism , Risk Factors , Bacteria/genetics , Butyrates , Kidney Calculi/microbiology
14.
Folia Microbiol (Praha) ; 69(2): 423-432, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38217756

ABSTRACT

Oxalate degradation is one of lactic acid bacteria's desirable activities. It is achieved by two enzymes, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). The current study aimed to screen 15 locally isolated lactic acid bacteria to select those with the highest oxalate degradation ability. It also aimed to amplify the genes involved in degradation. MRS broth supplemented with 20 mM sodium oxalate was used to culture the tested isolates for 72 h. This was followed by an enzymatic assay to detect remaining oxalate. All isolates showed oxalate degradation activity to variable degrees. Five isolates demonstrated high oxalate degradation, 78 to 88%. To investigate the oxalate-degradation potential of the selected isolates, they have been further tested for the presence of genes that encode for enzymes involved in oxalate catabolism, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). Three strains showed bands with the specific OXC and FRC forward and reverse primers designated as (SA-5, 9 and 37). Species-level identification revealed Loigolactobacillus bifermentans, Lacticaseibacillus paracasei, and Lactiplantibacillus plantarum. Preliminary results revealed that the tested probiotic strains harbored both oxc and frc whose products are putatively involved in oxalate catabolism. The probiotic potential of the selected strains was evaluated, and they showed high survival rates to both simulated gastric and intestinal fluids and variable degrees of antagonism against the tested Gram-positive and negative pathogens and were sensitive to clarithromycin but resistant to both metronidazole and ceftazidime. Finally, these strains could be exploited as an innovative approach to establish oxalate homeostasis in humans and prevent kidney stone formation.


Subject(s)
Acyl Coenzyme A , Carboxy-Lyases , Probiotics , Humans , Coenzyme A-Transferases/genetics , Coenzyme A-Transferases/metabolism , Carboxy-Lyases/genetics , Oxalates/metabolism
15.
J Phys Chem Lett ; 15(3): 725-732, 2024 Jan 25.
Article in English | MEDLINE | ID: mdl-38215403

ABSTRACT

Transporter proteins change their conformations to carry their substrate across the cell membrane. The conformational dynamics is vital to understanding the transport function. We have studied the oxalate transporter (OxlT), an oxalate:formate antiporter from Oxalobacter formigenes, significant in avoiding kidney stone formation. The atomic structure of OxlT has been recently solved in the outward-open and occluded states. However, the inward-open conformation is still missing, hindering a complete understanding of the transporter. Here, we performed a Gaussian accelerated molecular dynamics simulation to sample the extensive conformational space of OxlT and successfully predicted the inward-open conformation where cytoplasmic substrate formate binding was preferred over oxalate binding. We also identified critical interactions for the inward-open conformation. The results were complemented by an AlphaFold2 structure prediction. Although AlphaFold2 solely predicted OxlT in the outward-open conformation, mutation of the identified critical residues made it partly predict the inward-open conformation, identifying possible state-shifting mutations.


Subject(s)
Molecular Dynamics Simulation , Oxalates , Oxalates/chemistry , Oxalates/metabolism , Membrane Transport Proteins/chemistry , Antiporters/metabolism , Formates/metabolism , Protein Conformation
16.
J Inherit Metab Dis ; 47(2): 280-288, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38200664

ABSTRACT

Glyoxylate is a key metabolite generated from various precursor substrates in different subcellular compartments including mitochondria, peroxisomes, and the cytosol. The fact that glyoxylate is a good substrate for the ubiquitously expressed enzyme lactate dehydrogenase (LDH) requires the presence of efficient glyoxylate detoxification systems to avoid the formation of oxalate. Furthermore, this detoxification needs to be compartment-specific since LDH is actively present in multiple subcellular compartments including peroxisomes, mitochondria, and the cytosol. Whereas the identity of these protection systems has been established for both peroxisomes and the cytosol as concluded from the deficiency of alanine glyoxylate aminotransferase (AGT) in primary hyperoxaluria type 1 (PH1) and glyoxylate reductase (GR) in PH2, the glyoxylate protection system in mitochondria has remained less well defined. In this manuscript, we show that the enzyme glyoxylate reductase has a bimodal distribution in human embryonic kidney (HEK293), hepatocellular carcinoma (HepG2), and cervical carcinoma (HeLa) cells and more importantly, in human liver, and is actively present in both the mitochondrial and cytosolic compartments. We conclude that the metabolism of glyoxylate in humans requires the complicated interaction between different subcellular compartments within the cell and discuss the implications for the different primary hyperoxalurias.


Subject(s)
Alcohol Oxidoreductases , Mitochondria, Liver , Transaminases , Humans , Mitochondria, Liver/metabolism , HEK293 Cells , Oxalates/metabolism , Liver/metabolism , Glyoxylates/metabolism
17.
Drugs ; 83(18): 1729-1733, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38060091

ABSTRACT

Nedosiran (RIVFLOZA™), a once-monthly subcutaneous small interfering RNA (siRNA) therapy, is being developed by Dicerna Pharmaceuticals, a Novo Nordisk company, for the treatment of primary hyperoxaluria (PH). It reduces oxalate overproduction by inhibiting the expression of the hepatic lactate dehydrogenase (LDH) enzyme. Nedosiran received its first approval on 29 September 2023 in the USA to lower urinary oxalate levels in children aged ≥ 9 years and adults with PH type 1 (PH1) and relatively preserved kidney function [e.g. estimated glomerular filtration rate (eGFR) ≥ 30 mL/min/1.73 m2]. This article summarizes the milestones in the development of nedosiran leading to this first approval for PH1.


Subject(s)
Hyperoxaluria, Primary , Child , Adult , Humans , Hyperoxaluria, Primary/metabolism , Oxalates/metabolism , Lactate Dehydrogenases , RNA, Small Interfering
18.
Microbiome ; 11(1): 263, 2023 Nov 25.
Article in English | MEDLINE | ID: mdl-38007438

ABSTRACT

BACKGROUND: Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC), we provide a unified assessment of the bacterial contribution to KSD. RESULTS: Amplicon and shotgun metagenomic sequencing approaches were consistent in identifying multi-site microbiota disturbances in SF relative to HC. Biomarker taxa, reduced taxonomic and functional diversity, functional replacement of core bioenergetic pathways with virulence-associated gene markers, and community network collapse defined SF, but differences between cohorts did not extend to oxalate metabolism. CONCLUSIONS: We conclude that multi-site microbiota alteration is a hallmark of SF, and KSD treatment should consider microbial functional restoration and the avoidance of aberrant modulators such as poor diet and antibiotics where applicable to prevent stone recurrence. Video Abstract.


Subject(s)
Kidney Calculi , Microbiota , Humans , Microbiota/genetics , Oxalates/metabolism , Metagenome , Bacteria
19.
R I Med J (2013) ; 106(11): 14-19, 2023 Dec 01.
Article in English | MEDLINE | ID: mdl-38015779

ABSTRACT

Hyperoxaluria is a clinically relevant metabolic entity that portends a high morbidity burden. Primarily manifesting as kidney stone disease and chronic kidney disease, advanced hyperoxaluria can also affect major organs, including the brain, heart, liver, bone, and the skin. It is categorized based on etiology into primary and secondary hyperoxaluria. Pathology is attributed to excess de novo oxalate production in the former and multifactorial exogenous oxalate absorption or excess intake of its precursors in the latter. Diagnosis often involves demonstrating elevated urinary oxalate levels, especially in patients with normal kidney function. Here in this review, we will perform an in-depth discussion of various causes of hyperoxaluria and describe treatment options. In view of the significant morbidity burden associated with hyperoxaluria, patients could benefit from heightened clinician awareness to aid in the timely diagnosis and management of this condition.


Subject(s)
Hyperoxaluria , Kidney Calculi , Humans , Kidney Calculi/etiology , Kidney Calculi/urine , Hyperoxaluria/complications , Hyperoxaluria/diagnosis , Oxalates/metabolism
20.
Inflamm Res ; 72(12): 2111-2126, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37924395

ABSTRACT

OBJECTIVE AND DESIGN: Kidney stones commonly occur with a 50% recurrence rate within 5 years, and can elevate the risk of chronic kidney disease. Macrophage-to-myofibroblast transition (MMT) is a newly discovered mechanism that leads to progressive fibrosis in different forms of kidney disease. In this study, we aimed to investigate the role of MMT in renal fibrosis in glyoxylate-induced kidney stone mice and the mechanism by which signal transducer and activator of transcription 6 (STAT6) regulates MMT. METHODS: We collected non-functioning kidneys from patients with stones, established glyoxylate-induced calcium oxalate stone mice model and treated AS1517499 every other day in the treatment group, and constructed a STAT6-knockout RAW264.7 cell line. We first screened the enrichment pathway of the model by transcriptome sequencing; detected renal injury and fibrosis by hematoxylin eosin staining, Von Kossa staining and Sirius red staining; detected MMT levels by multiplexed immunofluorescence and flow cytometry; and verified the binding site of STAT6 at the PPARα promoter by chromatin immunoprecipitation. Fatty acid oxidation (FAO) and fibrosis-related genes were detected by western blot and real-time quantitative polymerase chain reaction. RESULTS: In this study, we found that FAO was downregulated, macrophages converted to myofibroblasts, and STAT6 expression was elevated in stone patients and glyoxylate-induced kidney stone mice. The promotion of FAO in macrophages attenuated MMT and upregulated fibrosis-related genes induced by calcium oxalate treatment. Further, inhibition of peroxisome proliferator-activated receptor-α (PPARα) eliminated the effect of STAT6 deletion on FAO and fibrosis-associated protein expression. Pharmacological inhibition of STAT6 also prevented the development of renal injury, lipid accumulation, MMT, and renal fibrosis. Mechanistically, STAT6 transcriptionally represses PPARα and FAO through cis-inducible elements located in the promoter region of the gene, thereby promoting MMT and renal fibrosis. CONCLUSIONS: These findings establish a role for STAT6 in kidney stone injury-induced renal fibrosis, and suggest that STAT6 may be a therapeutic target for progressive renal fibrosis in patients with nephrolithiasis.


Subject(s)
Kidney Calculi , Myofibroblasts , Animals , Humans , Mice , Calcium Oxalate/metabolism , Calcium Oxalate/pharmacology , Fatty Acids/metabolism , Fibrosis , Glyoxylates/metabolism , Glyoxylates/pharmacology , Kidney/pathology , Kidney Calculi/metabolism , Kidney Calculi/pathology , Macrophages/metabolism , Myofibroblasts/pathology , Oxalates/metabolism , Oxalates/pharmacology , PPAR alpha/metabolism , STAT6 Transcription Factor/genetics , STAT6 Transcription Factor/metabolism
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