2.1 Experimental animal
Twelve-week-old male mice were utilized in this study. Uox gene-deficient (Uox-KO) mice, bred on a C57BL/6J genetic background, were procured from Changzhou Cavens Laboratory Animal Limited Company. All procedures related to animal care and handling adhered to the guidelines established by the National Institutes of Health and received approval from the Animal Policy and Welfare Committee of the Naval Medical University. The mice were maintained in an environmentally controlled room set at a temperature of 22 ± 2.0°C and a relative humidity of 50% ± 5%, with a 12-hour light/dark cycle. They were provided with standard rodent chow and tap water.
2.2 Blood biochemistry tests
The serum was isolated from the collected blood samples by centrifugation at 3,000 × g for 15 minutes at 4°C for subsequent analysis. The concentrations of alanine aminotransferase (ALT), aspartate aminotransferase (AST), creatinine (Crea), blood urea nitrogen (BUN), urinary creatinine (BU), total cholesterol (TC), and triglycerides (TG) were quantified using an automated biochemical analyzer.
2.3 Histological analysis
The right kidney was excised and subsequently fixed in 4% paraformaldehyde (pH 7.4) for a minimum duration of 24 hours. Following fixation, the tissue underwent dehydration and was then embedded in paraffin wax. Sections were cut at a thickness of 4 micrometers and subjected to hematoxylin and eosin (H&E) staining as well as Masson's staining. The stained sections were examined under a light microscope to evaluate histopathological alterations.
2.4 Amino acidomics
2.4.1 2.4.1 Sample processing
Take 50μL of serum and mix it with 300μL of acetonitrile (L-2-chlorophenylalanine, 0.3 mg/mL), after vigorous shaking, centrifuge the sample for 10 min (12,000 rpm, 4°C), collect the supernatant and filter it through a needle filter (0.22 μm pore size) for LC-MS analysis.
2.4.2 LC-MS analysis
The analysis was performed using a Waters Xevo TQ-XS mass spectrometer (Waters Corporation, Manchester, UK). The sample solution was injected onto an ACQUITY UPLC™ AMID column (inner diameter 100 mm × 2.1 mm, film thickness 1.7 μm) at a flow rate of 300 μL/min. A gradient elution was performed using solution A (10 mM ammonium formate and 0.3% formic acid in water) and solution B (0.3% formic acid in acetonitrile). MS analysis was performed in positive ion mode using ESI and multiple reaction monitoring scans. The electrospray cone voltage was set at 3.2 kV, and the source temperature was maintained at 150 °C. The peak area of the internal standard was monitored for mass spectrometry. Internal standard peak areas were monitored for quality control and individual samples whose peak areas differed from the group mean by more than two standard deviations were reanalyzed. Automated peak integration was performed using the MarkerLynx Application Manager software (version 4.1; Waters Corporation, Milford, MA, USA). Finally, metabolites were identified by analyzing the metabolite peaks and comparing them against known standards.
2.4.3 Statistical analysis
The univariate analyses conducted comprised the Student's t-test and fold change (FC) analysis. For multivariate analyses, unsupervised principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were performed utilizing SIMCA-P version 14.0 software. The significance of differential metabolites (DMs) was determined by integrating predictor variable importance (VIP) values greater than 1 from the OPLS-DA model with P-values obtained from the Student's t-test. DMs were deemed significant when the VIP score exceeded 1 and the p-value was less than 0.05. Pathway enrichment analysis, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG), was conducted utilizing the MetaboAnalyst online platform[13].
2.5 Mendelian Randomization
2.5.1 Study design
This study is structured into two primary phases. In the initial phase, univariate Mendelian randomization (UVMR) was employed to evaluate the causal relationship between uric acid levels and various renal diseases, utilizing single nucleotide polymorphisms (SNPs) as instrumental variables for each exposure. In the subsequent phase, amino acid levels were selected as potential mediators in the causal pathway between uric acid levels and kidney disease. Ultimately, two-step multivariate Mendelian randomization (MVMR) was applied to quantify the mediating effects and proportions.
2.5.2 GWAS data sources
The dataset utilized in this study was sourced from the IEU GWAS database at the University of Bristol (https://gwasmrcieu.ac.uk). Regarding the exposure variables, data on serum uric acid levels were derived from a study conducted by Sakaue S, published in 2021, encompassing 343,836 samples and 19,041,286 SNPs[14].
For the mediator variables,data of alanine(Ala), glutamine(Gln), glycine(Gly), histidine(His), isoleucine(Ile), leucine(Leu), phenylalanine(Phe), tyrosine(Tyr), and valine(Val) were sourced from a study conducted by Richardson TG in 2021[15], data of arginine(Arg), asparagine(Asn), asparticacid(Asp), cysteine(Cys), glutamine(Glu), lysine(Lys), methionine(Met), proline(Pro), serine(Ser), threonine(Tyr), and tryptophan(Trp) from a study conducted by Shin in 2014[16].We selected the mediators between UA and kidney disease based on the following criteria:(I) There exists a causal association between UA and the mediator[17];The causal relationship between the mediator and the outcome must remain consistent regardless of whether UA is adjusted for; (III) The causal relationship between UA and the mediator should correspond with the causal relationship between the mediator and the outcome[12]. In the two-step Mendelian Randomization analysis, SNPs demonstrating genome-wide significance in the genome-wide association study (GWAS) of the mediator were identified following a linkage disequilibrium analysis, which applied a threshold of R² < 0.001 and a distance criterion of greater than 10,000 kilobases.
For the outcome variables, including the date of CRF and nephrotic syndrome, blood urea nitrogen levels were obtained from a study conducted by Sakaue in 2021[14], which analyzed 482,858 samples and 24,185,976 SNPs. The study on glomerulonephritis (GN) included 16,380,466 SNPs. The estimated glomerular filtration rate based on eGFRcr and eGFRcys, as well as the urinary albumin-to-creatinine ratio (UACR), were derived from the CKDGen Consortium. The fundamental characteristics of the genome-wide association studies (GWAS) from CKDGen were based on summary data reported by Pattaro C[18] and Teumer A et al[19].
Details of all data sources are provided in Table 1. Ethical approval from the relevant institutional review boards, informed consent from participants, and rigorous quality control measures were secured for all genome-wide association studies (GWASs). For this study, ethical approval was not necessary as the data utilized were at an aggregated level.
2.5.3 Statistical analysis
2.5.3.1 MR Analysis and Mediation Analysis
This study concentrated on employing MR analysis to elucidate the causal relationship between UA and kidney disease, with a specific focus on the pathways mediating this relationship. Initially, a bidirectional two-sample MR analysis was conducted, designating UA as the exposure variable and kidney disease as the outcome variable, to ascertain the causal linkage between these entities. Upon identifying a unidirectional causal relationship from UA to kidney disease, we proceeded to further investigate this association through mediated Mendelian analysis.
We employed IVW as the primary methodology for both UVMR and MVMR analyses. All Mendelian randomization analyses adhered to three essential assumptions: (1) Genetic variants must exhibit a strong association with the exposure in UVMR analyses and with at least one of the multiple exposures in MVMR analyses; (2) Genetic variants must not be associated with confounding factors that could influence the relationship between each exposure instrument and the outcome; (3) The impact of genetic variants on outcomes is mediated through each exposure.
In the context of mediation analysis, to evaluate whether amino acid mediators serve as intermediaries between uric acid and kidney disease, the initial step involved estimating the causal effect of genetically determined uric acid on the mediator (β1) using UVMR. The subsequent phase involved estimating the causal impact of the mediators on kidney disease through MVMR, with adjustments made for UA (β2), and the computation of F-values exceeding 10 to ensure the robustness of the findings. Following this, the indirect effect (β1 × β2) was divided by the overall causal effect of UA on kidney disease, as determined by UVMR (β), to ascertain the proportion of the total effect of UA attributable to AAS - mediated kidney disease (Fig. 1). Finally, we employ the Delta method to derive the standard error of the mediated proportion, utilizing the effect estimates obtained from the two-sample Mendelian Randomization analysis, and subsequently calculate the corresponding confidence intervals.
2.5.3.2 Sensitivity analyses
In order to assess the robustness of the IVW results in UVMR analysis, up to four MR methods—namely MR-Egger, weighted median, simple mode, and weighted mode—were employed, each of which assumes different models of pleiotropy. Similarly, in MVMR analysis, the MR-Egger, MR-Lasso, and median methods were utilized to validate the robustness of the IVW results. The findings indicated that at least one method consistently demonstrated significance in alignment with the direction of the IVW results. Notably, the MR-Egger method accounted for horizontal pleiotropy by incorporating the MR-Egger intercept[20]. The intercept signifies the mean pleiotropic effect across the genetic variants, representing the average direct effect of a variant on the outcome. A significant deviation of the intercept from zero indicated by an MR-Egger intercept P-value < 0.05) suggests the presence of horizontal pleiotropy. The validity of the instrument was assessed using the conditional F-statistic, with values exceeding 10 indicating a reduced likelihood of distortion in MR estimates due to weak instruments[21]. The Q' heterogeneity test was employed to statistically evaluate the heterogeneity among the instruments. This MR analysis was conducted using the TwoSampleMR package, version 0.5.8, within the R 4.3.1 framework.