Coding region analysis of vitamin D receptor gene and its association with active calcium stone disease

Genetic Polymorphisms and Kidney Stones Around the Globe: A Systematic Review and Meta-Analysis

Objective: This study explores associations between recurrent kidney stones and genetic polymorphisms.

Methods: Meta-analysis of polymorphisms in renal stone cases versus control groups. Four electronic databases (PubMed, SCOPUS, EMBASE, and Web of Science) were searched up to 30 May 2021, using the keywords: “kidney stone” or “kidney calculi,” or “urolithiasis” or “nephrolithiasis” or “urinary calculi” and “genome” or “genetic” or “mutation” or “single nucleotide polymorphism.” Forrest plots, ORs, 95% CI, Chi-square (χ2)-test, and index of heterogeneity (I2) were calculated. Only studies with Newcastle–Ottawa scale (NOS) ≥ 6 were included for quality control, and Funnel, Begg’s, and Eager’s plots assessed publication bias. PROSPERO: CRD42022250427.

Results: Among 7,671 searched articles, 72 were included. Polymorphisms in VDR (OR: 1.20; 95% CI: 1.06–1.36), CASR (OR = 1.24; 95% CI: 1.01–1.52), Osteopontin (OR = 1.38; 95% CI: 1.09–1.74), and Urokinase genes (OR = 1.52; 95% CI: 1.02–2.28) showed a significant association with risk of urinary stone formation, while Klotho gene showed a protective effect (OR = 0.75; 95% CI: 0.57–0.99). The VDR gene polymorphism was frequent in Asians, whereas CASR polymorphism was frequent in European and North American populations.

Conclusion: Multifactorial nature of the stone formation, emphasizing the role of environmental factors, might explain contradictory results in the literature. While polymorphisms in VDR, CASR, Osteopontin, and Urokinase genes were associated with urinary stone formation, the Klotho gene showed a protective effect.

CAG repeats and one polymorphism in androgen receptor gene are associated with renal calcium stone disease

PURPOSE

Evidence suggests that androgens can be involved in the pathogenesis of renal stones. This study aimed at investigating coding region polymorphisms and CAG repeats in androgen receptor (AR) and their association with active renal calcium stone disease.

MATERIALS AND METHODS

Male patients with calcium kidney stones (N = 106) with at least two episodes of stone recurrence or size increase during the past 5 years (ASF) were enrolled from December 2008 to April 2009. Control individuals were recruited after matching for age and gender from healthy individuals without current stone or history of stone disease. Genetic sequencing and single strand conformational polymorphism (SSCP) were used to determine AR polymorphisms in the patients and controls.

RESULTS

Two polymorphisms were identified in the AR gene: Silent G to A polymorphism in the first exon of the AR gene and C to G polymorphism in intron 4. CAG repeats ranged from 12 to 37. The C/G polymorphism in intron 4 and CAG repeats were associated with the status of active renal calcium stone disease (all p < 0.05). The CC variant of C/G polymorphism was not observed in patients with stone disease. CAG repeats less than 20 and more than 28 were mostly observed in ASF patients (p < 0.05).

CONCLUSIONS

CAG repeats and intron 4 C/G polymorphism in the AR gene have an association with renal calcium stone disease.

Genetic polymorphisms as prognostic factors for recurrent kidney stones: A systematic review and meta-analysis

Genetic polymorphisms have been suggested as risk factors affecting the occurrence and recurrence of kidney stones, although findings regarding the latter remain inconclusive. We performed this systematic review and meta-analysis to clarify the associations between genetic polymorphisms and recurrent kidney stones. PubMed, SCOPUS, EMBASE, and Cochrane Library databases were searched through May 28^th, 2020 to identify eligible studies. The Quality in prognostic studies (QUIPS) tool was used to evaluate bias risk. Allelic frequencies and different inheritance models were assessed. All analyses were performed using Review manager 5.4. A total of 14 studies were included for meta-analysis, assessing urokinase (ApaL1) and vitamin D receptor (VDR) (ApaI, BsmI, FokI, and TaqI) gene polymorphisms. The ApaLI polymorphism demonstrated protective association in the recessive model [odds ratio (OR) 0.45, P < 0.01] albeit higher risk among Caucasians in the heterozygous model (OR 16.03, P < 0.01). The VDR-ApaI polymorphism showed protective association in the dominant model (OR 0.60, P < 0.01). Among Asians, the VDR-FokI polymorphism recessive model showed significant positive association (OR 1.70, P < 0.01) and the VDR-TaqI polymorphism heterozygous model exhibited protective association (OR 0.72, P < 0.01). The VDR-BsmI polymorphism was not significantly associated with recurrent kidney stones in any model. Urokinase-ApaLI (recessive model), VDR-ApaI (dominant model), and VDR-TaqI (heterozygous model) polymorphisms were associated with decreased recurrent kidney stone risk whereas urokinase-ApaLI (heterozygous model) and VDR-FokI polymorphisms were associated with increased risk among Caucasians and Asians, respectively. These findings will assist in identifying individuals at risk of kidney stone recurrence.

Vitamin D receptor gene polymorphisms and susceptibility to urolithiasis: a meta-regression and meta-analysis

BACKGROUND

The currently available data with respect to the association between vitamin D receptor (VDR) gene polymorphism and risk to urolithiasis are inconclusive and inconsistent. Hence, an exhaustive meta-analysis can solve the discrepancies and provide a hint for upcoming investigations. Herein, a meta-analysis was carried out to attain a conclusive estimate of the association between VDR gene single nucleotide polymorphisms (SNPs) and urolithiasis risk.

METHODS

The major databases, including ISI Web of science, Scopus, and PubMed/MEDLINE were searched systematically from until June 2020 to retrieve all relevant studies. Association between VDR gene polymorphisms, including FokI (rs2228570), TaqI (rs731236), BsmI (rs1544410), and ApaI (rs7975232), and urolithiasis risk was evaluated using pooled odds ratio (OR) and their corresponding 95% confidence interval (CI). Additionally, to seek for the potential source of heterogeneity, meta-regression analyses were exerted.

RESULTS

Literature search led to finally finding of 33 studies evaluating the VDR gene SNPs and urolithiasis risk. It was observed that none of the four SNPs were significantly associated with urolithiasis predisposition. However, subgroup analysis confirmed higher risk of urolithiasis in East-Asian and Caucasian population with ApaI and TaqI gene polymorphism. The analyses of sensitivity acknowledged the results stability.

CONCLUSION

Although this meta-analysis did not support the association of FokI, TaqI, BsmI, and ApaI in the overall polled analysis, it suggests that ApaI and TaqI SNPs is associated with increased risk of urolithiasis in East-Asian and Caucasians populations.

Relationship Between the ApaI (rs7975232), BsmI (rs1544410), FokI (rs2228570), and TaqI (rs731236) Variants in the Vitamin D Receptor Gene and Urolithiasis Susceptibility: An Updated Meta-Analysis and Trial Sequential Analysis

The relationship between urolithiasis and vitamin D receptor (VDR) gene variants is still under debate according to the available published literature. To assess correlations between VDR gene variants ApaI (rs7975232), BsmI (rs1544410), FokI (rs2228570), and TaqI (rs731236) and urolithiasis susceptibility, we performed the present study through meta-analysis. The PubMed, Cochrane Library, China National Knowledge Infrastructure, EMBASE, Web of Science, and Wanfang databases were searched to retrieve qualified case-control studies. Finally, 31 reports were selected for the present meta-analysis. The results demonstrated that the VDR gene TaqI TT genotype was related to decreased risk of urolithiasis in the overall population (TT vs. Tt+tt: P = 0.011, OR = 0.824, 95% CI = 0.709–0.957). In ethnicity subgroup analysis, we found that the TaqI variant was obviously correlated to urolithiasis risk among Asians and Caucasians (P < 0.05). Additionally, significant urolithiasis risk was identified in adults. However, the FokI, BsmI, and ApaI variants did not have an increased risk of developing urolithiasis. Trial sequential analysis results were on a sufficiently large number of participants and did not require more research to confirm associations. Our research suggested that the VDR gene variant TaqI was correlated with urolithiasis susceptibility and that the t-allele might be the risk gene and T-allele the protective gene in VDR TaqI variant.

Genetic factors of polygenic urolithiasis

The article summarizes the findings of Russian and international studies of the genetic aspects of polygenic urolithiasis associated with impairment of calcium metabolism. The article analyzes the genetic risk factors of polygenic nephrolithiasis that show significant association with the disease in case-control studies and Genome-Wide Association Studies (16 genes). We described the gene functions involved in concrement formation in polygenic nephrolithiasis. The modern molecular and genetic technologies (DNA microarray, high-throughput DNA sequencing, etc.) enable identification of the genetic predisposition to a specific disease, realization of the individualized treatment of the patient, and carrying out timely preventive measures among the proband's relatives.

The rs1256328 (ALPL) and rs12654812 (RGS14) Polymorphisms are Associated with Susceptibility to Calcium Nephrolithiasis in a Taiwanese population

Nephrolithiasis is a common disease affecting almost all populations, with an increasing prevalence over the past decades. Previous studies revealed several functional polymorphisms associated with the pathogenesis of nephrolithiasis. However, data on Asian populations are limited. In this study, three candidate polymorphisms were selected from previous studies to investigate the correlations with nephrolithiasis in a Taiwanese population. In total, 454 nephrolithiasis patients were recruited from Kaohsiung Medical University Hospital, with SNP frequency for 1513 subjects of general population from the Taiwan Biobank (TWB) as a genotypic reference. Results revealed that subjects with minor TT genotype at rs1256328 (alkaline phosphatase, liver/bone/kidney (ALPL)) have higher susceptibility to nephrolithiasis (odds ratio (OR) = 2.03, p = 0.0013). In addition, subjects carrying the minor AA genotype at rs12654812 (regulator of G protein signaling 14 (RGS14)) have higher susceptibility to nephrolithiasis (OR = 1.91, p = 0.0017). Among nephrolithiasis patients, subjects with GG at rs7627468 (calcium-sensing receptor (CASR)) have lower pH level in urine (p = 0.0088). Importantly, rs7627468 is associated with the expressions of IQCB1 and EAF2. rs12654812 could influence the expression of RGS14 itself, MXD3, and FGFR4. In summary, this study successfully validated the genetic roles of rs1256328 and rs12654812 in human nephrolithiasis.

Association of vitamin D receptor gene polymorphisms and risk of urolithiasis: results of a genetic epidemiology study and comprehensive meta-analysis

Polymorphisms of vitamin D receptor (VDR) gene have been associated with risk of urolithiasis, but, with inconsistent results and lack data from Pakistani population. Therefore, after including our indigenous study data, a comprehensive meta-analysis was performed to provide an evidence-based estimate of any association between VDR polymorphisms and urolithiasis risk. A total of 483 Pakistani subjects, comprising 235 urolithiasis patients and 248 healthy controls, were genotyped for 6 VDR polymorphisms. Additionally, a systematic literature search with subsequent meta-analysis was conducted and pooled odds ratios (ORs) were used to determine the strength of any existent associations. Trial sequential analysis (TSA) was also performed. Results revealed no significant association of any VDR polymorphism and urolithiasis risk in indigenous Pakistani patients. However, meta-analysis of 29 relevant studies indicated that VDR FokI polymorphism significantly increased the risk of urolithiasis in allelic (f vs. F: OR = 1.13; 95% CI = 1.05-1.22; p ≤ 0.01) and recessive (ff vs. FF + Ff: OR = 1.20; 95% CI = 1.05-1.38; p = 0.01) models with no significant heterogeneity. No associations were evident for VDR ApaI, BsmI and TaqI polymorphic variants and urolithiasis risk after correction for multiple testing. Subgroup analysis by ethnicity suggested significant association for FokI variant among Asians. The TSA results demonstrated that the evidence reflecting association of FokI polymorphism and urolithiasis risk was sufficient and conclusive. In conclusion, this meta-analysis suggests that VDR FokI polymorphism is significantly associated with urolithiasis risk, especially in Asians, whereas ApaI, BsmI and TaqI polymorphisms are not associated.

Association between vitamin D receptor gene polymorphisms and idiopathic hypocitraturia in a Chinese Bai population

Idiopathic hypocitraturia (IH) is a risk factor for urolithiasis. IH is associated with vitamin D receptor (VDR) gene single nucleotide polymorphisms (SNPs) in a Chinese Han population. However, this association between VDR SNPs and IH has not been recapitulated in a Chinese Bai population. The aim of this study is to investigate the association between VDR SNPs and IH in a Chinese Bai population. A total of 320 participants comprising of 200 Chinese Bai patients with IH and 120 Chinese Bai control participants with normal urinary citrate level were enrolled for this study. The VDR SNPs rs7975232, rs2228570, rs731236 and rs1544410 were detected by Sanger sequencing, and the association between these SNPs and the presence of IH in the Chinese Bai population was analyzed. The prevalence of VDR SNPs rs7975232 allele A and rs2228570 genotype TT was significantly higher in patients than in controls (p < 0.0125, after Bonferroni correction). The haplotype TCGC was a protective factor in the Chinese Bai population who otherwise might suffer from IH, while the haplotype TTGA was a risk factor. VDR SNPs rs731236 and rs1544410 have a linkage disequilibrium value of 0.811. VDR SNPs rs7975232, rs2228570, and haplotypes TCGC, TTGA are associated with IH in a Chinese Bai population.

Etiologic risk factors and vitamin D receptor gene polymorphisms in under one-year-old infants with urolithiasis

The incidence of urinary tract stones in infancy has been increasing in Turkey. Risk factors and vitamin D receptor (VDR) gene polymorphisms were investigated in infants aged < 1 year who had stones. Forty infants with urinary tract stones and 80 infants without stones, aged < 1 year were enrolled in this study. Detailed surveys were taken of all infants, metabolic parameters and ApaI and FokI VDR gene polymorphisms were investigated. Infants with stones tended to be more commonly fed formula and multivitamins (vitamins A, C, D) (p < 0.05). Positive family history came into prominence in the stony group (p < 0.05). There were no significant differences in ApaI and FokI VDR gene polymorphisms between the groups with stones and the control groups. However, CA genotype of ApaI polymorphism was associated with family history and C allele of ApaI was related with family history and hypercalciuria (p < 0.05). Hypercalciuria emerged as an underlying metabolic abnormality in the etiology of stones, and was observed at a rate of 38%. Infants who are given formula and multivitamins for vitamin D supplementation are at increased risk for the formation of urinary tract stones. VDR gene polymorphisms cause the formation of urinary tract stones and affect calcium (Ca) metabolism.

Genetic Risk Factors for Idiopathic Urolithiasis: A Systematic Review of the Literature and Causal Network Analysis

CONTEXT

Urolithiasis has a high prevalence and recurrence rate. Prevention is key to patient management, but risk stratification is challenging. In particular, genetic predisposition for urinary stones is not fully understood.

OBJECTIVE

To review current evidence of potential causative genes for idiopathic urolithiasis and map their relationships to one another. This evidence is essential for future establishment of molecular targeted therapy.

EVIDENCE ACQUISITION

A systematic literature review from 2007 to 2017 was performed in accordance with the Preferred Reporting Items for Systematic Review and Meta-analyses guidelines. The search was restricted to human studies conducted as either case-control or genome-wide association studies, and published in English. We also performed a causal network analysis of candidate genes gained from the systematic review using Ingenuity Pathway Analysis (IPA).

EVIDENCE SYNTHESIS

During the systematic screening of literature, 30 papers were selected for the review. A total of 20 genes with 42 polymorphisms/variants were found to be associated with urolithiasis risk. Their functional roles were mainly categorized as stone matrix, calcium and phosphate regulation, urinary concentration and constitution, and inflammation/oxidative stress. IPA network analysis revealed that these genes connected via signaling pathways and a proinflammatory/oxidative environment.

CONCLUSIONS

This systematic review provides an updated gene list and novel causal networks for idiopathic urolithiasis risk. Although some genes such as SPP1, CASR, VDR, CLDN14, and SLC34A1 were identified by several studies and recognized by prior reviews, further investigation elucidating their roles in stone formation will be essential for future studies.

PATIENT SUMMARY

In this review, we summarized recent literature regarding genes responsible for kidney stone risk. Based on a detailed review of 30 articles and computational network analysis, we concluded that disorder of mineral regulation with local inflammation in the kidney may cause kidney stone disease.

ApaL1 urokinase and Taq1 vitamin D receptor gene polymorphisms in first-stone formers, recurrent stone formers, and controls in a Caucasian population

The purpose of this study was to determine differences in genotype distribution and allele frequency of urokinase and vitamin D receptor (VDR) single nucleotide polymorphisms (SNPs) between first-stone formers, recurrent stone formers, and controls in a Caucasian population. A total of 86 first-stone formers, 78 recurrent stone formers, and 167 controls were included. Urokinase and VDR SNPs were tested by gene amplification followed by ApaL1 and Taq1 endonuclease digestion, respectively. Baseline variables, genotype, and allele frequencies were compared between the three groups, using descriptive statistics. Adjusted odds ratios were calculated to estimate the risk for recurrent urolithiasis associated with genotypes. We found that differences in the distribution of ApaL1 SNP and Taq1 SNP genotypes were statistically different between recurrent stone formers and first-stone formers, and between recurrent stone formers and controls. Allele frequency analysis showed that the T allele for ApaL1 SNP and the C allele for Taq1 SNP were significantly associated with recurrent urolithiasis. For Taq1 SNP, logistic regression analysis showed that the C/C genotype was associated with a more than threefold higher risk for recurrent urolithiasis. We conclude that ApaL1 and Taq1 SNPs of the urokinase and VDR genes are associated with recurrent urolithiasis in a Caucasian population.

Effects of vitamin D receptor polymorphisms on urolithiasis risk: a meta-analysis

Background

Several studies analyzed the associations of Vitamin D receptor (VDR) polymorphisms with urolithiasis risk in different ethnic groups. However, the results were inconclusive. To evaluate a more precise estimation of the relationship, a meta-analysis was performed.

Methods

Pubmed, EMBASE, Wanfang Database, China National Knowledge Infrastructure (CNKI) and Weipu Database were searched. Data were extracted independently by two investigators. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of associations.

Results

Twenty-three case–control studies were included in this meta-analysis. Significant associations between ApaI, BsmI, FokI, and TaqI polymorphisms and urolithiasis risk were observed. However, sensitivity analyses for BsmI and FokI polymorphisms indicated that the results were not reliable and credible. In addition, there was a significant association of the ApaI-TaqI haplotype with urolithiasis risk.

Conclusions

This meta-analysis suggested that ApaI and TaqI polymorphisms in VDR gene were associated with urolithiasis risk.