Dataset Information

Urinary proteins from stone formers promote calcium oxalate crystallization, growth and aggregation via oxidative modifications

ABSTRACT: Various urinary parameters have been used to determine kidney stone risk. However, almost all of the widely used lithogenic indices rely on urinary concentrations of small molecules/ions and pH. We hypothesized that urinary macromolecules (especially proteins) also play a critical role in determining the stone risk. Herein, we purified the complexed urinary proteins (proteome) from healthy individuals and calcium oxalate (CaOx) stone formers and performed various crystal assays and quantitative proteomics to compare them. While the normal urinary proteome inhibited CaOx stone-forming mechanisms (i.e., crystallization, growth and aggregation), the stone formers’ urinary proteome promoted all these CaOx crystal parameters. Descriptive proteomics by nanoLC-ESI-LTQ-Orbitrap-MS/MS analysis identified 203 and 381 proteins in the urine of healthy individuals and stone formers, respectively. Analyses of physicochemical properties revealed only molecular mass and isoelectric point that slightly increased in the stone formers’ urine, whereas instability index, grand average of hydrophathicity (GRAVY) and amino acid composition were comparable. Interestingly, proportion of oxidatively modified proteins (particularly those with methionine oxidation, methionine dioxidation and cysteine trioxidation) markedly increased (~2.5-fold) in the stone formers’ urine. Quantitative proteomics revealed 89 increased and 56 decreased proteins in the stone formers’ urine. The oxidized proteins had a greater proportion (>3-fold) in the increased proteins (77%) compared with the decreased ones (23%), whereas the non-oxidized proteins showed comparable proportions (54% and 46%, respectively). Functional enrichment analyses revealed a correlation between the increased proteins and oxidative stress biological processes and molecular functions. Finally, ELISA confirmed the significantly increased levels of oxidized proteins in the stone formers’ urine compared with that of healthy individuals. These data implicate that oxidatively modified proteome serves as the key pathogenic factor or risk for CaOx kidney stone formation.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

SUBMITTER: Visith Thongboonkerd

LAB HEAD: Prof. Visith Thongboonkerd

PROVIDER: PXD050609 | Pride | 2026-03-09

REPOSITORIES: Pride

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Urinary proteins from stone formers promote calcium oxalate crystallization, growth and aggregation via oxidative modifications.

Hadpech Sudarat S Peerapen Paleerath P Chaiyarit Sakdithep S Sritippayawan Suchai S Thongboonkerd Visith V

Journal of advanced research 20250523

<h4>Introduction</h4>Various urinary parameters are used for determining kidney stone risk. However, almost all of the widely used lithogenic indices rely on urinary concentrations of small molecules/ions and pH.<h4>Objective</h4>To address whether urinary macromolecules (especially oxidatively modified proteins) also play a critical role in determining the stone risk.<h4>Methods</h4>Complexed urinary proteins (proteome) were purified from healthy individuals and calcium oxalate (CaOx) stone for ...[more]

PMID: 40414344

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Project description:Pseudomonas aeruginosa is one of the most frequent pathogen dominant in complicated urinary tract infections (UTI). To unravel the adaptation strategies of P. aeruginosa to the conditions in the urinary tract and to define the underlying regulatory network an artificial growth system mimicking the conditions in the urinary tract was established. Transcriptome analyses were used to investigate the physiological status of P. aeruginosa under this conditions. We performed comparisons to identify genes induced under artificial urinary tract conditions to unravel the adaptive strategies and the underlying regulatory network used by Pseudomonas aeruginosa during urinary tract infections using Affimetrix GeneChips. Pseudomonas aeruginosa wild type strain PAO1 was grown in an artificial in vitro growth system mimicking the conditions in the urinary tract. Therefore, biofilms were grown on the surface of membrane filters placed on agar plates at 37 Â°C up to the late logarithmic state under aerobic and anaerobic conditions (incubated in an anaerobic beanch). An artificial urine medium (AUM) simulating the averaged urine of an human adult was used as nutrient souce. 10-fold diluted Luria Bertani (LB)-medium was used as reference medium. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. The biofilms were harveted at this time points and resuspsended in 0.9% (w/v) NaCl. The OD578 of biofilm suspension was 0.8 for all tested conditions. First comparison: Identification of genes induced or repressed under aerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown aerobically for 18 h to the late logarithmic phase in biofilms on AUM with the transcriptome profile of the PAO1 strain, which was grown aerobically for 18 h to the late logarithmic phase in biofilms on 10-fold diluted LB. Second comparison: Identification of genes induced or repressed under anaerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown anaerobically for 2 days up to the late logarithmic phase in biofilms on AUM supplemented with 50 mM nitrate with the transcriptome profile of the PAO1 strain, which was grown anaerobically for 2 days up to the late logarithmic phase in biofilms on 10-fold diluted LB supplemented with 50 mM nitrate.

			Action	DRS
	Healthy1.raw	Raw
	Healthy2.raw	Raw
	Healthy3.raw	Raw
	StoneFormer1.raw	Raw
	StoneFormer2.raw	Raw