Evidence for epistatic interaction between VDR and SLC13A2 genes in the pathogenesis of hypocitraturia in recurrent calcium oxalate stone formers

Whole-genome scan for selection signature associated with temperature adaptation in Iranian sheep breeds

The present study aimed to identify the selection signature associated with temperature adaptation in Iranian sheep breeds raised in cold and hot environments. The Illumina HD ovine SNP600K BeadChip genomic arrays were utilized to analyze 114 animals from eight Iranian sheep breeds, namely Ghezel, Afshari, Shall, Sanjabi, Lori-Bakhtiari, Karakul, Kermani, and Balochi. All animals were classified into two groups: cold-weather breeds and hot-weather breeds, based on the environments to which they are adapted and the regions where they have been raised for many years. The unbiased FST (Theta) and hapFLK tests were used to identify the selection signatures. The results revealed five genomic regions on chromosomes 2, 10, 11, 13, and 14 using the FST test, and three genomic regions on chromosomes 10, 14, and 15 using the hapFLK test to be under selection in cold and hot groups. Further exploration of these genomic regions revealed that most of these regions overlapped with genes previously identified to affect cold and heat stress, nervous system function, cell division and gene expression, skin growth and development, embryo and skeletal development, adaptation to hypoxia conditions, and the immune system. These regions overlapped with QTLs that had previously been identified as being associated with various important economic traits, such as body weight, skin color, and horn characteristics. The gene ontology and gene network analyses revealed significant pathways and networks that distinguished Iranian cold and hot climates sheep breeds from each other. We identified positively selected genomic regions in Iranian sheep associated with pathways related to cell division, biological processes, cellular responses to calcium ions, metal ions and inorganic substances. This study represents the initial effort to identify selective sweeps linked to temperature adaptation in Iranian indigenous sheep breeds. It may provide valuable insights into the genomic regions involved in climate adaptation in sheep.

Association of single nucleotide genetic polymorphisms of vitamin D receptor and calcium-sensitive receptor with calcium-containing kidney stones in Chinese Dai populations: a prospective multi-center study

PURPOSE

To evaluate the association between vitamin D receptor (VDRs) and calcium-sensitive receptor (CaSR) gene polymorphisms and calcium-containing kidney stones (CCKS) in Dai populations.

METHODS

A total of 160 CCKS patients and 87 healthy controls were included in this study. CCKS was confirmed using urological computed tomography (CT), plain abdominal radiograph, or surgical lithotomy. Stone samples obtained during surgery were analyzed using infrared spectroscopy. Venous blood and 24-h urine samples were collected and analyzed using Sanger sequencing and high-performance liquid chromatography, respectively. Genetic variants in the VDR gene (rs7975232, rs2228570, rs731236, and rs1544410) and CaSR gene (rs7652589, rs1801725, and rs1042636) were identified through sequence analysis.

RESULTS

Analysis of genotype and allele frequencies revealed that the rs7975232 polymorphism in the VDR gene and the rs7652589 allele in the CaSR gene were significantly associated with CCKS. Furthermore, patients carrying the AC and AA genotypes of rs7975232 showed a higher incidence of hypocitraturia compared to those with other genotypes (p < 0.05). The AA and GG genotypes of rs1042636 and the AA genotype of rs7652589 were significantly associated with hypercalciuria (p < 0.05).

CONCLUSION

CCKS in this study population may be closely related to hypocitraturia caused by the VDR locus rs7975232 polymorphism and hypercalciuria caused by the CaSR locus rs1042636 and rs7652589 polymorphism.

A functional MMP-9-1562C>T polymorphism, MMP-9 serum levels and nephrolithiasis risk in a southern Chinese population

Background

The role of matrix metalloproteinase 9 (MMP-9) in the pathophysiology of chronic kidney disease (CKD), which is associated with a nearly two-fold greater risk for urinary calculi compared to people without CKD, has been demonstrated. The aim of the research is to evaluate the association between MMP-9-1562C>T polymorphism, MMP-9 serum levels and nephrolithiasis risk.

Methods

A hospital-based case-control study involving 302 kidney stone patients and 408 controls without kidney stone from southern China was conducted. Sanger sequencing was used to genotype the MMP-9-1562C>T polymorphism. The serum MMP-9 was measured in 105 kidney stone patients and 77 controls by enzyme-linked immunosorbent assay.

Results

Compared to the control group, the CT genotype was more frequent in nephrolithiasis patients (adjusted OR = 1.60, 95% CI = 1.09-2.37: the risk of developing nephrolithiasis in individuals with CT genotype compared to CC genotype). Moreover, there was also a higher frequency of CT/TT genotypes among patients with nephrolithiasis (adjusted OR = 1.49, 95% CI = 1.02-2.19: the risk of developing nephrolithiasis in individuals with CT/TT genotypes compared to CC genotype). The risk remained for the subgroups of patients aged >53, smokers with pack-years of smoking >20, non-drinkers, non-diabetic patients, patients with hypertension, recurrent episodes and calcium oxalate stones (OR = 2.26, 95% CI = 1.31-3.91; OR = 5.47, 95% CI = 1.10-27.30; OR = 1.76, 95% CI = 1.14-2.72; OR = 1.54, 95% CI = 1.03-2.30; OR = 1.97, 95% CI = 1.01-3.82; OR = 1.67, 95% CI = 1.06-2.62; OR = 1.54, 95% CI = 1.02-2.32, respectively). Biochemical parameters did not differ between genotypes. Compared to controls (18.57 ± 5.80 ng/mL), nephrolithiasis patients had significantly higher serum MMP-9 levels (30.17 ± 6.78 ng/mL, p < 0.001). The serum MMP-9 levels of patients with CT/TT genotypes of MMP-9-1562C>T were significantly higher than those with CC genotype (32.00 ± 6.33 vs. 29.13 ± 6.85 ng/mL, p = 0.037).

Conclusion

The MMP-9-1562C>T polymorphism in association with its soluble protein increased the risk of kidney stone, thus suggesting it could be used as a susceptibility biomarker for nephrolithiasis. Further functional studies and larger studies that include environmental exposure data are needed to confirm the findings.

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.

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.

Idiopathic Osteoporosis and Nephrolithiasis: Two Sides of the Same Coin?

Idiopathic osteoporosis and nephrolithiasis are formidable health problems showing a progressive increase in their incidence and prevalence in the last decades. These temporal trends were observed in both pediatric and adult populations worldwide. Epidemiological and experimental studies indicate that both disorders show several common pathogenic environmental and genetic factors. In this review, we analyzed the clinical characteristics common to the two disorders and the state-of-the-art knowledge regarding the genetic predisposition and the environmental factors recognized as triggers in adult and pediatric ages. As a result of this work, we propose to consider idiopathic nephrolithiasis and osteoporosis as two possible expressions of a unique clinical syndrome. Accordingly, the clinical approach to both disorders should be modified in order to program an efficient primary and secondary prevention strategy.

Vitamin D Status in Paget Disease of Bone and Efficacy-Safety Profile of Cholecalciferol Treatment in Pagetic Patients with Hypovitaminosis D

Adequate vitamin D status is essential for skeletal health. Paget's disease of bone (PDB) is a common metabolic skeletal disorder, but data regarding the vitamin D status in PDB patients are lacking. We performed a case-control study to estimate vitamin D status in 708 PDB patients and in 1803 healthy controls from Italy and an observational prospective study to evaluate the efficacy-safety profile of oral cholecalciferol treatment [400.000 International Units (UI) of cholecalciferol administered in cycles of 8 weeks until 25OHD levels reaches 70 nmol/L as primary therapy and 50.000 UI of cholecalciferol administered every 2 weeks for 52 weeks for the maintenance therapy] in 82 PDB patients with hypovitaminosis D, i.e., 25OHD < 50 nmol/L. The main outcome measures for the prospective study were 25OHD levels, metabolic risk factors (RF) for nephrolithiasis, bone pain score (BPS), and pain medication score (PMS). Over half of PDB patients had hypovitaminosis D. Among PDB patients treated with cholecalciferol, 76 patients reached 25OHD levels ≥ 70 nmol/L after the first cycle of primary therapy and the remaining six patients after a second cycle. The maintenance therapy guaranteed 25OHD levels ≥ 70 nmol/L during the entire follow-up. The increase in 25OHD levels reduced PTH, BPS, and PMS levels, without changes in RF for nephrolithiasis. We can conclude that (i) hypovitaminosis D is frequent in PDB patients, (ii) cholecalciferol significantly increased 25OHD levels in PDB patients, and (iii) the correction of hypovitaminosis D improves the quality of life of PDB patients without inducing significant changes in RF for 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.

Polymorphisms of the VDR gene in patients with nephrolithiasis in a Han Chinese population

An association study between VDR gene polymorphisms and nephrolithiasis was conducted in different populations, but it is not yet known whether the association exists in the Han Chinese population. Here, we genotyped three SNPs (rs731236, rs7975232 and rs10735810) in the promoter region of the VDR gene by iMLDR genotyping assays in a large case-control cohort. The results demonstrated that there was no association found between the three SNPs (rs731236, rs7975232 and rs10735810) in the VDR gene and nephrolithiasis, whether in allele or genotype distribution. However, SNP rs10735810 was correlated with the level of serum calcium in control groups, but not in patient groups. In conclusion, considering the large sample size, we believe that the SNP rs10735810 allele A in the VDR gene promoter region may influence the level of serum calcium, but not influence the formation of nephrolithiasis in a Han Chinese population.