Allele-frequency determination of BsmI and FokI polymorphisms of the VDR gene by quantitative real-time PCR (QRT-PCR) in pooled genomic DNA samples

The relationship between vitamin D receptor gene polymorphism and deciduous tooth decay in Chinese children

Background

In the present study, we explored the link between vitamin D receptor (VDR) BsmI, TaqI, ApaI and FokI gene polymorphisms with deciduous tooth decay in Chinese children.

Methods

Our study included 380 Chinese children aged 4–7 years, whose DNA sample was collected from the buccal mucosa. VDR gene polymorphisms was determined by PCR-RFLP.

Results

The adjusted logistic regression analysis demonstrated that BsmI containing the Bb genotype was linked with the increased risk of deciduous tooth decay (OR = 1.856, 95% CI = [1.184, 2.908], p = 0.007). However, VDR polymorphisms ApaI, TaqI and FokI were not associated with deciduous tooth decay (ApaI: OR = 0.839, 95% CI = [0.614, 1.145], p = 0.268; TaqI: OR = 1.150, 95% CI = [0.495, 2.672], p = 0.744; FokI: OR = 0.856, 95% CI = [0.616, 1.191], p = 0.356).

Conclusions

Our results showed that VDR BsmI polymorphism was associated with the risk of deciduous tooth decay in Chinese children aged 4–7 years. However, the specific mechanism remains to further verify through experiment.

Influence of Vitamin D Receptor Gene Fok1 Polymorphism on Bone Mass Accrual Post Calcium and Vitamin D Supplementation

OBJECTIVE

To examine the association of vitamin D receptor (VDR) gene polymorphisms of the Fok1 locus on bone mass accrual in Indian girls used to a low calcium intake.

METHODS

An intervention trial was undertaken in 102 girls aged 8-16 y, attending a state run school in Pune city, India. All girls received 500 mg calcium daily and 30,000 IU of vitamin D3 quarterly for one year. Dietary calcium intake was evaluated. Bone mineral content (BMC), bone area (BA) and bone mineral density (BMD) were measured at total body using Dual Energy X-ray Absorptiometry (Lunar DPX-PRO). Polymorphisms of the Fok1 locus of the vitamin D Receptor (VDR) gene were detected using SYBR Green quantitative polymerase chain reaction.

RESULTS

The prevalence of Fok1 polymorphism was 43.1% (Ff), 9.8% (ff) and 47.1% (FF). At baseline, FF genotype had significantly lower BMD as compared to ff and Ff genotype (p < 0.05). At baseline, majority of girls (82.4%) were hypocalcemic with low calcium intake. Post-supplementation, FF genotype had significantly lower bone mass as compared to ff and Ff genotype. Significant increase in BMC [Ff (17.9%); ff (18.1%); FF (17.4%)], and BMD [Ff (5.4 %); ff (6.3%); FF (4.8%)] was observed post supplementation (p value < 0.05), though percentage increase in BMC and BMD was similar for three Fok1 polymorphisms (p > 0.1).

CONCLUSIONS

VDR gene polymorphism, as defined by Fok1 genotype had no positive influence on bone mass accrual in response to calcium supplementation.

Influence of ethnicity on the distribution of genetic polymorphisms associated with risk of chronic liver disease in South American populations

BACKGROUND

The global burden of chronic liver disease is rising. Besides environmental, behavioral, viral and metabolic factors, genetic polymorphisms in patatin-like phospholipase-3 (PNPLA3) and vitamin D receptor (VDR) genes have been related to the development of chronic liver disease and progression towards liver cancer. Although their prevalence differs remarkably among ethnic groups, the frequency of these polymorphisms in South American populations -whose genetic background is highly admixed- has been poorly studied. Hence, the aim of this study was to characterize polymorphisms related to chronic liver disease and their association with the genetic ancestry of South American populations.

RESULTS

DNA samples from 258 healthy unrelated male volunteers were analyzed. The frequencies of G and C alleles of rs738409 polymorphism (PNPLA3 gene) were 74 % and 26 %, respectively; whereas the bAt (CCA) haplotype (VDR gene) was observed in 32.5 % of the samples. The GG genotype of PNPLA3 rs738409 and the bAt (CCA) haplotype -associated with an increased risk of chronic liver disease and progression towards liver cancer- were significantly more frequent among samples exhibiting maternal and paternal Native American haplogroups (63.7 % and 64.6 %), intermediate among admixed samples (45.1 % and 44.9 %; p = 0.03) and the lowest for Non-native American ancestry (30.1 % and 29.6 %; p = 0.001 and p = 0.0008).

CONCLUSIONS

These results suggest that individuals with Native American ancestry might have a high risk of chronic liver disorders and cancer. Furthermore, these data not only support the molecular evaluation of ancestry in multi-ethnic population studies, but also suggest that the characterization of these variants in South American populations may be useful for establishing public health policies aimed at high risk ethnic communities.

Vitamin D receptor gene polymorphisms and bone mass indices in post-menarchal Indian adolescent girls

To study the association between vitamin D receptor (VDR) gene polymorphisms and bone mass indices in adolescent girls, a cross-sectional study was conducted in 120 post-menarchal girls aged 15-18 years in Pune city, India. Serum levels of ionised calcium, inorganic phosphorous, parathyroid hormone and 25-hydroxy vitamin-D were measured. Bone mineral content (BMC), bone area (BA) and bone mineral density (BMD) were measured at total body (TB), lumbar spine (LS) and left femoral neck (FN) using dual energy X-ray absorptiometry. Polymorphisms of the VDR gene at the Fok1 and Bsm1 loci were detected using SYBR Green quantitative polymerase chain reaction. The overall distribution of genotypes at the Bsm1 locus in this study was 33.3 % Bb, 29.2 % bb and 37.5 % BB while that for the Fok1 locus was 44.2 % Ff, 7.5 % ff and 48.3 % FF. There were no significant differences in the blood parameters when classified according to Bsm1 or Fok1 genotypes. Subjects with BB genotype have significantly higher mean TBBMC, TBBA, TBBMD and LSBMD than Bb and bb (p < 0.05) and showed a tendency for association with LSBMC and LSBA (p < 0.1). Subjects with Ff genotype showed a tendency for association with left FNBMC and FNBA (p < 0.1). Bsm1 genotype did not show an association with FN bone indices whereas Fok1 genotype did not show association with TB or LS bone indices. In conclusion, the present study demonstrates VDR gene polymorphism, defined by Bsm1 genotype, has an influence on total body and lumbar spine bone mass indices in post-menarchal Indian girls.

Bone mass and biochemical markers of bone turnover in children and adolescents with chronic immune thrombocytopenia: relation to corticosteroid therapy and vitamin D receptor gene polymorphisms

Optional drug therapy in refractory chronic immune thrombocytopenia (ITP) includes standard oral, pulsed high-dose steroid therapy, intravenous gamma globulin, anti-D, and immunosuppressive therapy or thrombopoietin receptor agonists. This work aimed to study the bone mass in children and adolescents with chronic ITP in relation to biochemical markers of bone turnover, cumulative steroid therapy, and the possible modulating effect of vitamin D receptor (VDR) gene polymorphisms. Thirty-six children and adolescents with chronic ITP were recruited from the Hematology Clinic, Children's Hospital, Ain Shams University and the Hematology Clinic of the National Research Centre in Egypt and compared with 43 healthy age- and sex-matched controls. The total cumulative dose of steroids was calculated. Bone markers (serum osteocalcin (OC) and propeptide I precollagen (PICP) and urinary deoxypyridinoline (DPD) excretion), analysis of VDR gene distribution, and dual energy X-ray absorptiometry at lumbar and hip regions were performed for patients and controls. Compared to controls, chronic ITP patients had higher body mass index (BMI) and lower height for age standard deviation score (SDS). Chronic ITP patients had lower levels of OC and C-terminal propeptide of type I procollagen (PICP) and higher urinary DPD excretion, and bone mineral density (BMD) was significantly lower for both spine and hip z-score (<0.001). BMD was inversely correlated with urinary DPD excretion, age, BMI, and cumulative steroid dose. There was significant negative correlation between cumulative oral steroid dose and BMD (r = -0.4, P = 0.01 and r = -0.45, p = 0.001 for spine and hip z-scores, respectively), but the correlation was non-significant in relation to cumulative pulsed steroid therapy. FokI polymorphism was significantly related to BMD for both spine and hip z-score (p = 0.015 and p = 0.008, respectively), but there was no relation between BMD and Bsm1 polymorphism. FokI gene polymorphism may be one of the contributing factors in bone loss in patients on chronic steroid therapy. High cumulative doses of corticosteroids increased bone resorption in young chronic ITP patients. Longitudinal studies are needed to confirm the effect of different steroid protocols on bone turnover. Protocols of therapy of chronic ITP should restrict corticosteroid use in growing children and favor alternative less harmful therapies.

Predictors of bone disease in Egyptian prepubertal children with β-thalassaemia major

INTRODUCTION

Thalassaemic osteopathy is a multifactorial disorder and limited information exists about bone accrual and bone mineral density (BMD) in prepubertal thalassaemic children. The study aimed to investigate some potential genetic and biochemical bone markers as possible early predictors of BMD variations in children with β-thalassaemia major (TM) before puberty.

MATERIAL AND METHODS

Thirt-one prepubertal children with β-TM, and 43 matched controls were subjected to BMD assessment by dual energy X-ray absorptiometry (DEXA). Vitamin D receptor (VDR) gene polymorphisms (Bsm1, Fok1) and the biochemical bone markers serum osteocalcin and propeptide I procollagen (CPIP) and urinary deoxypyridinoline (DPD) excretion were assessed.

RESULTS

Bone mineral density was reduced in 25% of thalassaemics at the spine and 15.4% at the hip region. Significantly higher levels of urinary DPD and lower serum osteocalcin and CPIP levels were found in the studied thalassaemic children compared to controls (p < 0.001). A significant negative correlation was present between BMD in spine and hip and the patients' age (r = -0.6367, p = 0.0002 and r = -0.616, p = 0.00079, respectively). There was a significant reduction in BMD in males compared to females. Reduced BMD was more frequent in male patients with genotypes bb and Ff but not in females. Bone mineral density was not related to the studied biochemical bone markers, mean pre-transfusion haemoglobin or serum ferritin.

CONCLUSIONS

Routine BMD screening with DEXA is proposed to be a sensitive predictor for early bone changes, particularly at the lumbar spine. DR gene polymorphisms of Bsm1 and Fok1 polymorphisms may be determinants of BMD in Egyptian prepubertal male thalassemics.

The vitamin D receptor gene BsmI polymorphism is not associated with anthropometric and biochemical parameters describing metabolic syndrome in postmenopausal women

AIM

Vitamin D could have a direct effect on adipocyte differentiation and metabolism and might be involved in glucose regulation of insulin secretion. In recent years several polymorphisms in the gene encoding the vitamin D receptor (VDR), which are potent to alter the activity of VDR protein, have been described. The present study aimed to investigate the prevalence of the VDR BsmI polymorphism and its association with anthropometric and biochemical features of metabolic syndrome in postmenopausal women.

MATERIALS AND METHODS

We studied 351 randomly selected healthy postmenopausal women, with mean age of 55.43 +/- 2.75 years and mean body mass index (BMI) of 27.5 +/- 4.78 kg/m2, to evaluate the frequency of BsmI polymorphism (by restriction fragment length polymorphism-polymerase chain reaction) in the VDR gene and to find out whether there is an association between this polymorphism and BMI, total fat volume and visceral fat (as determined by total body dual-energy X-ray absorptiometry), blood pressure, lipid profile (total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, triglycerides) glucose and fasting insulin in the whole group, as well as subgroups of obese and non-obese women.

RESULTS

The prevalence of BsmI genotypes in the study group was 51.0% Bb, 37.3% bb and 11.7% BB. Genotype distribution did not differ from that expected under Hardy-Weinberg equilibrium conditions (chi2 = 2.95, p = 0.22). Apart from LDL-C levels (F = 3.46, p = 0.032), there were no significant differences in anthropometric or metabolic parameters between genotypes.

CONCLUSIONS

The BsmI polymorphism in the VDR gene does not seem to predispose to obesity and insulin resistance, but the BB genotype is connected with an unfavorable lipid profile.

Genotypes and clinical aspects associated with bone mineral density in Argentine postmenopausal women

The aim of this study was to determine genotypes and clinical aspects associated with bone mineral density (BMD) in postmenopausal women from Córdoba, Argentina. Polymorphisms were assessed by RFLP-PCR technique using BsmI and FokI for vitamin D receptor gene (VDR) and XbaI and PvuII for estrogen receptor-alpha gene (ERalpha) as restrictases. Sixty-eight healthy, 54 osteopenic, and 64 osteoporotic postmenopausal women were recruited. Femoral neck and lumbar spine BMD were inversely correlated with age in the entire analyzed population. Height was lower in osteopenic and osteoporotic women as compared to healthy women (P < 0.05). Weight and body mass index (BMI) were the lowest in osteoporotic women (P < 0.01 versus healthy group). Serum procollagen type I Nterminal propeptide (PINP) was higher in osteoporotic women as compared to the other groups. Distribution of VDR and ERalpha genotypes was similar in the three groups. Genotype bb (VDR) was associated with low values of lumbar BMD in the healthy group (P < 0.05 versus genotype Bb), and with low values of femoral BMD (P < 0.05 versus genotype BB) in osteoporotic women. BB*Pp interaction was associated with the highest femoral neck BMD (P < 0.05), whereas the bb*xx interaction was associated with the lowest femoral neck BMD in the total population analyzed (P < 0.05). In conclusion, parameters such as age, height, weight, BMI, serum PINP, VDR genotypes, and interactions between VDR and ERalpha genotypes could be useful to predict a decrease in BMD in Argentine postmenopausal women.

Molecular genetic studies of gene identification for osteoporosis: a 2004 update

This review summarizes comprehensively the most important and representative molecular genetics studies of gene identification for osteoporosis published up to the end of December 2004. It is intended to constitute a sequential update of our previously published review covering the available data up to the end of 2002. Evidence from candidate gene association studies and genome-wide linkage studies in humans, as well as quantitative trait locus mapping animal models are reviewed separately. Studies of transgenic and knockout mice models relevant to osteoporosis are summarized. An important extension of this update is incorporation of functional genomic studies (including DNA microarrays and proteomics) on osteogenesis and osteoporosis, in light of the rapid advances and the promising prospects of the field. Comments are made on the most notable findings and representative studies for their potential influence and implications on our present understanding of genetics of osteoporosis. The format adopted by this review should be ideal for accommodating future new advances and studies.

Individual single tube genotyping and DNA pooling by allele-specific PCR to uncover associations of polymorphisms with complex diseases

BACKGROUND

The genotyping for the study of the SNPs in different complex diseases require a great number of patients. In this sense, the determination of allele frequencies and genotypes requires a rapid and economical procedure.

METHODS

The genotype has been carried out by allele-specific PCR in single tube with the discrimination of the products of PCR by its T(m). For this purpose a GC tail was added to 5' extreme of the specific primer. The allele frequencies were also calculated by DNA pooling and QRT-PCR using allele-specific primers.

RESULTS

The use of the genotyping in single tube through allele-specific PCR and melting curves has led us to the accurate genotype of three polymorphisms of vdr (cdx-2), osteoprotegerin (A-163G) and ppar-gamma (C-681G) genes in 225 postmenopausal women to be associated to osteoporosis. Only the cdx-2 polymorphism was associated with a reduced bone mineral density (BMD). These data were similar to those obtained when the allele frequencies were calculated using QRT-PCR in DNA pools.

CONCLUSIONS

Individual genotyping with allele-specific PCR in single tube and melting curve analysis is a fast, trustworthy and economic method to study any SNP. We propose the following approach to determine the possible association of SNPs with complex and multifactorial diseases like osteoporosis, in which hundreds of individuals should be analyzed: construct control and problem groups, make DNA pools, and calculate pooled allelic frequencies. Genotyping each individual further permits to determine the genotypic distribution when differences in allelic frequencies are observed, thus allowing more complex statistical analyses (including other variables like age, weight, etc.).