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Genetic variations, gene expression, and urinary metabolomic data related to purine and pyrimidine metabolism in Polish controls and patients with nephrolithiasis

Version 1.0

Wigner-Jeziorska, Paulina, 2026, "Genetic variations, gene expression, and urinary metabolomic data related to purine and pyrimidine metabolism in Polish controls and patients with nephrolithiasis", https://doi.org/10.18150/U7KJIR, RepOD, V1

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Description

Nephrolithiasis is one of the most common urological disorders worldwide, and its aetiology remains multifactorial and not fully understood. Both environmental and genetic factors are considered to contribute to the formation of urinary stones. In addition to well-established risk factors such as dietary habits, fluid intake, and body mass index, increasing evidence suggests that inherited disturbances in metabolic pathways, particularly those related to citrate and purine metabolism, may significantly influence susceptibility to urolithiasis.

Therefore, this study aimed to investigate the potential association between selected seven single-nucleotide polymorphisms (SNPs) in genes involved in purine and citrate metabolism - rs7279549 (T>C) – GART, rs2304497 (T>G) and rs80715753 (A>G) – ACLY, rs1713420 (A>G) – PNP, rs1884725 (A>G) and rs2295475 (G>A) – XDH, rs6634990 (T>G) – HPRT - and the development of nephrolithiasis in a Polish population. Genotyping was performed using TaqMan SNP genotyping assays. Moreover, we verified the association of urolithiasis development and mRNA expression of HPRT, PNP, XDH, ACLY and GART in peripheral blood mononuclear cells (the evaluation of mRNA expression was performed using real-time PCR and 2-ΔCt methods). Moreover, metabolomic profiling of urine samples was carried out using nuclear magnetic resonance (NMR) spectroscopy to determine the concentrations of selected metabolites associated with purine and citrate metabolism, including citrate, hypoxanthine, and glycine.

The presented experiments were conducted in cooperation with the Department of Urology of the Provincial Hospital of M. Kacprzak in Płock. In this study, it has been qualified 112 patients with urolithiasis hospitalised at the Department of Urology of the Provincial Hospital of M. Kacprzak in Płock and a homologous group of 114 healthy volunteers based on consent Bioethics Committee of the University of Lodz No. 12/KBBN-UŁ/II/2020-21 and the Bioethics Committee of the Medical University of Łódź (approval no. RNN/141/21/KE). The data were obtained for the project, the aim of which was to identify potential prognostic markers of urolithiasis. 

(2023-03-31)
Subject
Medicine, Health and Life Sciences
Keyword

urolithiasis, purine metabolism, mRNA expression, polymorphism, urine metabolites

CC0 Creative Commons Zero 1.0 CC0 Creative Commons Zero 1.0

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ReadMe.txt
Plain Text - 4.0 KB - Apr 8, 2026 - 0 Downloads
MD5: cb9420d81e248ee52c1d82cefe749816
License: CC0 Creative Commons Zero 1.0
Detailed description of data and procedures for all included files
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SNPs_data_control_and_urolithiasis_IDUB_csv.tab
Tabular Data - Original format: Comma Separated Values - 16.1 KB - Apr 8, 2026 - 0 Downloads
License: CC0 Creative Commons Zero 1.0
12 Variables, 226 Observations - UNF:6:HjlEhXYTF6Edh4utwxuJug==
SNPs (single nucleotide polymorphism) profiling of patients with urolithiasis (n=112) and controls (n=114) (csv version)
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mRNA_expression_level_data_control_and_urolithiasis_IDUB_csv.tab
Tabular Data - Original format: Comma Separated Values - 19.6 KB - Apr 8, 2026 - 0 Downloads
License: CC0 Creative Commons Zero 1.0
10 Variables, 226 Observations - UNF:6:Vx/vc2E5oGiUgvtVZNYhpA==
HPRT, PNP, XDH, ACLY and GART gene expression (n control =114, n patients with urolithiasis = 112) (csv version)
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metabolomic_analysis_using_NMR_spectroscopy.zip
ZIP Archive - 373.2 MB - Apr 8, 2026 - 0 Downloads
MD5: 516d1344cd90f238e636433ac7116c53
License: CC0 Creative Commons Zero 1.0
This repository contains raw metabolite quantification data generated directly by the analytical software Chenomx NMR Suite 8.1 (Chenomx Inc., Edmonton, AB, Canada). The dataset includes NMR spectra using the Chenomx profiling tools. The values presented in these files represent the direct output exported from the software without additional post-processing or statistical transformation. Metabolite identification and quantification were performed using the Chenomx compound library and internal fitting algorithms provided within the software environment.
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metabolomic_analysis_using_NMR_spectroscopy_csv.tab
Tabular Data - Original format: Comma Separated Values - 14.1 KB - Apr 8, 2026 - 0 Downloads
License: CC0 Creative Commons Zero 1.0
8 Variables, 226 Observations - UNF:6:5lQcYfn7LOTXzzPpP61axg==
the calculated concentrations of selected urinary metabolites (citrate, glycine, and hypoxanthine) derived from the raw data located in the folder (zip) named “metabolomic_analysis_using_NMR_spectroscopy” (csv version)
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