VDR FokI Research Articles

Association of vitamin D receptor gene polymorphisms with BMD and their effect on 1, 25-dihydroxy vitamin D3 levels in pre- and postmenopausal South Indian women from Andhra Pradesh

Background Osteoporosis is a multifactorial disorder with a strong genetic component and vitamin D receptor gene has been suggested as a candidate gene for osteoporosis. Therefore the present study was aimed to investigate the role of the VDR Fok 1 gene polymorphism and its influence on vitamin D3 levels and BMD in pre- and postmenopausal osteoporotic women of Indian ethnicity. Methods 427osteoporotic women and 460 age matched controls were included in the study. VDR FOK1 gene polymorphism was assessed by the PCR-RFLP method. Serum vitamin D3 was measured by the HPLC method. Results The frequency of ff genotype and f allele was significantly high in pre- and postmenopausal osteoporotic women in comparison with controls (p < 0.001).In each case individuals with ff genotype had significantly low BMD in comparison with Ff and FF genotypes. No significant association was found between the genotypes and vitamin D3 levels. Conclusion The VDR Fok 1 gene is associated with low bone mass in all our study subjects. The genotype ff of the VDR Fok 1 gene is associated with osteoporosis. Further ff genotype associated significantly with low bone mass. Therefore the f allele of VDR Fok1 gene is an important risk factor for osteoporosis.

Role of genetic pattern on bone mineral density in thalassemic patients

Objectives To evaluate the role of genetic background in osteoporosis/osteopenia development in beta-Thalassemia Major patients. Design and methods The influence of VDR ( FokI, BsmI) as well as COLIA1 (Sp1) gene polymorphisms on BMD was investigated in 40 patients. Results Although the examined gene polymorphisms did not significantly affect BMD variations in our population, BsmI was found to display beneficial effects on patient response to alendronate therapy. Conclusion Genetic factors retain a potential role for improvement of osteoporosis management in thalassemic patients.

Circulating 25-Hydroxyvitamin D, VDR Polymorphisms, and Survival in Advanced Non–Small-Cell Lung Cancer

We showed previously that in early-stage non-small-cell lung cancer (NSCLC), serum vitamin D levels and VDR polymorphisms were associated with survival. We hypothesized that vitamin D levels and VDR polymorphisms may also affect survival among patients with advanced NSCLC. We evaluated the relationship between circulating 25-hydroxyvitamin D levels; VDR polymorphisms, including Cdx-2 G>A (rs11568820), FokI C>T (rs10735810), and BsmI C>T (rs144410); and overall survival among patients with advanced NSCLC. Analyses of survival outcomes were performed using the log-rank test and Cox proportional hazards models, adjusting for sex, stage, and performance status. There were 294 patients and 233 deaths, with median follow-up of 42 months. We found no difference in survival by circulating vitamin D level. The C/C genotype of the FokI polymorphism was associated with improved survival: median survival for C/C was 21.4 months, for C/T was 12.1 months, and for T/T was 15.6 months (log-rank P = .005). There were no significant effects on survival by the Cdx-2 or BsMI polymorphism. However, having increasing numbers of protective alleles was associated with improved survival (adjusted hazard ratio for two or more v zero to one protective alleles, 0.57; 95% CI, 0.41 to 0.79; P = .0008). On haplotype analysis, the G-T-C (Cdx-2-FokI-BsmI) haplotype was associated with worse survival compared with the most common haplotype of G-C-T (adjusted hazard ratio, 1.61; 95% CI, 1.21 to 2.14; P = .001). There was no main effect of vitamin D level on overall survival in the advanced NSCLC population. The T allele of the VDR FokI>T polymorphism and the G-T-C (Cdx-2-FokI-BsmI) haplotype were associated with worse survival.

Clinical and genetic risk factors for bone loss in breast cancer survivors after adjuvant chemotherapy

578 Background: Premature ovarian failure and accelerated bone loss are common late effects of adjuvant chemotherapy for breast cancer. Polymorphisms (SNPs) in bone metabolism and estrogen biosynthesis genes associated with osteoporosis in the general population have been identified (COL1A1 Sp1, IL6_634, VDR fok1 & taq1, ESR1_397, ESR1_325, ESR Xba1, TGF-B 509 & 869). Little is known about clinical and genetic risk factors for osteoporosis in breast cancer survivors. Methods: We performed a cohort study at the Abramson Cancer Center of the University of Pennsylvania. Eligible patients were female, premenopausal at breast cancer diagnosis, AJCC stage I, II or III, had recent follow-up with no recurrence, and received adjuvant chemo one to four years prior to enrollment. Subjects signed informed consent, completed questionnaires, provided blood samples for genomic DNA, and underwent bone density measurement via DEXA scan as part of usual clinical care. Single nucleotide polymorphisms were identified via pyrosequencing and SNPlex assays. Results: We enrolled 132 breast cancer survivors with an average age at chemo start of 43 (range 26.7–57.8); 89% were Caucasian, 5% black. DEXAs were obtained on 118 (89%) at 1.9 years post-chemo (range 0–4.7). Most patients (94%) were treated with anthracycline-based regimens; 57% received a taxane. Hormone therapy was given to 76%; 12% received an aromatase inhibitor. Chemo-related amenorrhea occurred in 47% and was significantly associated with increasing age at chemo (p<0.0001). DEXAs were obtained at 41 facilities. Osteopenia/porosis (T-score < -1.0) at hip and/or spine occurred in 44 patients (33%). Increasing age at chemo was associated with a nonsignificant increase in the risk of osteopenia/porosis (OR 1.03, 95%CI 0.97, 1.1). Significant protective effects were found among women treated with a taxane (OR 0.45; 95%CI 0.21, 0.98), but dose density (q2 vs. q3wk) was not significant (OR 1.44, 95%CI 0.66, 3.2). SNP frequencies ranged from 16–96%; none were associated with osteopenia/porosis at this early timepoint. Conclusions: Age, dose density, and presence of high-risk SNPs were not associated with osteopenia/porosis among breast cancer survivors in the early post-chemotherapy period. Taxanes may have a protective effect. No significant financial relationships to disclose.

TotalPlex gene amplification using bulging primers for pharmacogenetic analysis of acute lymphoblastic leukemia

Genetic polymorphism among patients with acute lymphoblastic leukemia (ALL) is an important factor in the effectiveness and toxicity of anti-leukemic drugs. Genotyping of various polymorphisms that impact the outcome of anti-leukemic drug therapy (pharmacogenetics) presents an attractive approach for developing individualized therapy. We developed an easy and accurate method of analyzing multiple genes using a small amount of DNA, which we termed TotalPlex amplification. We used 16 pairs of specific bulging specific primers (SBS primers) for simultaneous amplification of 16 loci in a single PCR tube. Sixteen single nucleotide polymorphisms (SNPs) (CYP3A4*1B A>G, CYP3A5*3 G>A, GSTP1 313 A>G, GSTM1 deletion, GSTT1 deletion, MDR1 exon 21 G>T/A, MDR1 exon 26 C>T, MTHFR 677 C>T, MTHFR 1298 A>C, NR3C1 1088 A>G, RFC 80 G>A, TPMT 238 G>C, TPMT 460 G>A, TPMT 719 A>G, VDR intron 8 G>A, VDR FokI T>C) that have been implicated in the pharmacogenetics of ALL therapy were analyzed by TotalPlex amplification and SNP genotyping. We successfully amplified specific gene fragments using 16 pairs of primers in one PCR reaction tube with minimal spurious amplification products using TotalPlex amplification coupled to a multiplexed bead array detection system. The genotypes of 16 loci from 34 different genomic DNA (gDNA) samples derived using the TotalPlex system were consistent with the results of several standard genotyping methods, including automatic sequencing, PCR restriction fragment length polymorphism (RFLP) analysis, PCR, and allele-specific PCR (AS-PCR). Thus, the TotalPlex system represents a useful method of amplification that can improve the time, cost, and sample size required for high-throughput pharmacogenetic analysis of SNPs.

Relationship between vitamin D receptor BsmI and FokI polymorphisms and anthropometric and biochemical parameters describing metabolic syndrome

Introduction. It was found that vitamin D may have a direct effect on adipocyte differentiation and metabolism and might be involved in the glucose regulation of insulin secretion, as suggested from the discovery of a nuclear localization of 1,25-(OH)2D3 in pancreatic islets. In recent years, several polymorphisms in the VDR gene which are able to alter the activity of VDR protein have been described. The BsmI and FokI polymorphisms were described in relation to obesity and type 2 diabetes.The aim of the study was to find whether there are associations between BsmI and FokI polymorphisms and anthropometric (BMI, WHR, BP) and biochemical parameters describing metabolic syndrome.Materials and methods. Studied were 176 randomly selected men aged 25–65 years (mean: 51.99 years) with a mean BMI of 28.06 kg/m2. Two polymorphisms of the VDR gene (FokI and BsmI) were explored using the PCR-RFLP method. Serum glucose, insulin, total cholesterol, LDL, HDL, and TG were measured using commercially available kits.Results. It was found that BB carriers tend to have higher BMI (29.00 ± 3.74 versus 26.81 ± 3.76, p = 0.024) and waist circumference (101.79 ± 10.59 versus 96.23 ± 10.35, p = 0.014) compared with the bb genotypes. Similarly, FF and Ff carriers had higher fasting insulin levels than the ff genotypes (12.30 ± 10.26 versus 9.76 ± 5.88, p = 0.001 and 9.76 ± 5.88 vs. 6.35 ± 2.64, p = 0.008), and lover cHDL levels in comparison to ff genotypes (52.28 ± 10.02 versus 60.63 ± 16.58, p = 0.015 and 53.70 ± 12.03 versus 60.63 ± 16.58, p = 0.032. Besides these, no significant differences were found.Conclusions. The BsmI VDR polymorphism seems to influence BMI, while the FokI VDR polymorphism appears to affect insulin sensitivity and serum cHDL level.

How valid is single nucleotide polymorphism (SNP) diagnosis for the individual risk assessment of breast cancer? / Welchen Stellenwert hat der diagnostische Einsatz von Einzelnukleotid-Polymorphismen (SNPs) bei der individuellen Risikoeinschätzung von Brustkrebs?

Abstract The number of reports investigating disease susceptibility based on the carriage of low-penetrance, high-frequency single nucleotide polymorphisms (SNPs) has increased over the last years. Evidence is accumulating defining specific individual variations in breast cancer susceptibility. Genetic variations of the estradiol and xenobiotic metabolisms, as well as genes involved in cell cycle control, have been described as significant contributors to breast cancer susceptibility with variations depending on ethnic background and co-factors such as smoking and family history of breast cancer. In sum, the highest level of evidence to date linking SNPs and breast cancer comes from nested case-control studies within the prospective Nurses' Health Study. These data establish seven SNPs – hPRB +331 G/A, AR CAG repeat, CYP 19 TTTA(10), CYP 1A1 Msp I, VDR FOK1, XRCC1 Arg194Trp, and XRCC2 Arg188His – as small, but significant risk factors for spontaneous, non-hereditary breast cancer. In addition, meta-analysis of data in the literature established the TGFBR1*6A, the HRAS1, GSTP Ile105Val, and the GSTM1 SNPs as low-penetrance genetic risk factors for sporadic breast cancer. The clinical consequences of such a risk elevation may be a detailed instruction of the patient as to general measures of breast cancer prevention such as a low-fat diet, optimization of the BMI, physical exercise, avoidance of alcohol and long-term hormone replacement therapy (HRT), and participation in a breast cancer screening program between the age of 50 and 70 years. Specific surgical or drug interventions such as prophylactic mastectomy and oophorectomy or prophylactic intake of tamoxifen are not indicated based on SNP analysis at this time.

How valid is single nucleotide polymorphism (SNP) diagnosis for the individual risk assessment of breast cancer?

The number of reports investigating disease susceptibility based on the carriage of low-penetrance, high-frequency single nucleotide polymorphisms (SNPs) has increased in recent years. Evidence is accumulating defining specific individual variations in breast cancer susceptibility. Genetic variations of estradiol and xenobiotics metabolisms as well as genes involved in cell-cycle control have been described as significant contributors to breast cancer susceptibility, with variations depending on ethnic background and co-factors such as smoking and family history of breast cancer. In sum, the highest level of evidence to date linking SNPs and breast cancer comes from nested case–control studies within the prospective Nurses' Health Study. These data establish seven SNPs – hPRB +331G/A, AR CAG repeat, CYP19 (TTTA)10, CYP1A1 MspI, VDR FOK1, XRCC1 Arg194Trp and XRCC2 Arg188His – as small but significant risk factors for spontaneous, non-hereditary breast cancer. In addition, meta-analysis of data in the literature establishes the TGFBR1*6A, HRAS1, GSTP Ile105Val and GSTM1 SNPs as low-penetrance genetic risk factors of sporadic breast cancer. The clinical consequences of such a risk elevation may be detailed instruction of the patient as to general measures of breast cancer prevention such as a low-fat diet, optimization of body mass index, physical exercise, avoidance of alcohol and long-term hormone replacement therapy, and participation in a breast cancer screening program between the ages of 50 and 70 years. Specific surgical or drug interventions such as prophylactic mastectomy and oophorectomy or prophylactic intake of tamoxifen are not indicated based on SNP analysis at this time.

Association of vitamin-D and calcitonin receptor gene polymorphism in paediatric nephrolithiasis

We investigated the role of vitamin-D receptor gene (VDR) and calcitonin receptor (CTR) gene polymorphism in childhood nephrolithiasis in the north Indian population. A control group of 60 healthy paediatric individuals (age range 4-16 years) and 50 paediatric patients (age range 2-14 years) with kidney stones were examined. Polymorphism in both genes (VDR and CTR) was detected by using PCR-based restriction analysis. There was a statistically significant difference between the two groups for the genotypes of the VDR gene Fok-I polymorphism (P =0.007) and the CTR gene (P =0.048) polymorphism. The odds ratio (95% Confidence Interval) for the C allele in those at risk of stone disease was 1.83 (0.82-4.09) in VDR gene polymorphism and 1.99 (0.90-4.39) in the case of CTR gene polymorphism. Our results suggest that the effects of VDR (Fok-I) and CTR gene polymorphism contribute to the understanding of the pathogenesis of urinary calculi. It is also suggestive of a potential candidate gene in the search for genetic causes of paediatric calcium oxalate nephrolithiasis.

Association of Vitamin D Receptor-Gene (FokI) Polymorphism with Calcium Oxalate Nephrolithiasis

Formation of kidney stones is still not understood but is hypothesized to be associated with the vitamin D receptor gene (VDR). In order to assess the eventual role of VDR start-codon FokI polymorphism in stone formation, we evaluated the association between calcium stone disease and this polymorphism in a North Indian population. A control group comprised of 166 healthy individuals (age range 22-58 years) and a group of 138 patients with calcium oxalate stones (age range 21-72 years) were examined. The polymorphism was detected using polymerase chain reaction-based restriction analysis. An unexcisable length of 265 bp (CC) and two fragments of 169 bp and 96 bp (TT) were obtained by FokI restriction digestion. There was a statistically significant difference between the control and patient groups (X2 test, P<0.001) for the genotype of the VDR FokI start-codon polymorphism. The odds ratio (with 95% CI) for the C allele in those at risk of stone disease was 1.654 (1.041, 2.628). The VDR frequency distribution was also statistically significant (P<0.001) in case of male sex. The frequency distribution for this genetic polymorphism was not statistically different in normocalciuric and hypercalciuric stone patients (P=0.355). The VDR FokI polymorphism may be a good candidate for a marker for calcium oxalate-stone disease. These findings may contribute a small piece to the understanding of the pathogenesis of urinary calculi.

Vitamin D Receptor Gene Polymorphisms and Association with Type 2 Diabetes Mellitus in a Polish Population

Vitamin D plays an important role in insulin secretion. There is also evidence that this steroid may influence the insulin sensitivity. Thus genes involved in its metabolic pathway have been regarded as good candidates for type 2 diabetes mellitus (T2DM). One of them is vitamin D receptor gene (VDR). Its multiple polymorphisms have been examined for the association with T2DM in several populations. Those studies did not provide clear answers about the role of VDR in this disease. The aim of the study was to search for the association of FokI, ApaI, BsmI, and TaqI polymorphisms of VDR gene with T2DM in a Polish population using a case-control study design. Overall, 548 individuals were examined: 308 T2DM patients and 240 control individuals. The study groups were genotyped for VDR FokI, ApaI, BsmI, and TaqI variants using the restriction fragment length polymorphism (RFLP) method. Since variants of ApaI, BsmI, and TaqI polymorphisms were in very strong linkage disequilibrium, three loci haplotypes could be assigned to phase-unknown individuals with a high degree of confidence. Differences in allele, genotype, haplotype, and haplotype combination distribution between the groups were examined by chi2 test. The VDR allele frequencies for T2DM patients and controls were as follows: FokI-F/f - 53.4 %/46.6 % vs. 55.2 %/44.8 %, BsmI-B/b - 34.4 %/65.6 % vs. 37.5 %/62.5 %, ApaI-A/a - 47.9 %/52.1 % vs 50.9 %/49.1 %, TaqI-T/t - 67.6 %/32.4 % vs. 62.7 %/37.3 %, respectively. There was no difference between the groups in allele frequency. Similarly, distribution of genotypes, three locus BsmI/ApaI/TaqI haplotypes and their combinations were similar in the groups. In conclusion, our study did not provide evidence for the association of four examined VDR polymorphisms with T2DM in a Polish population. We postulate that to fully determine whether the sequence differences in VDR gene are susceptibility variants for T2DM, additional studies in different populations are required in a large study group.

The study of CTLA‐4 and vitamin D receptor polymorphisms in the Romanian type 1 diabetes population

Several studies suggested that part of the genetic susceptibility for Type 1 diabetes (T1DM) is encoded by some polymorphisms of CTLA-4 gene (2q33) and of Vitamin D Receptor gene (VDR; 12q12-14). Our aim was to assess their contribution to T1DM genetic susceptibility in the Romanian population. We typed CTLA-4 49 A/G and VDR FokI (F/f), ApaI (A/a) and TaqI (T/t) polymorphisms by Sequence Specific Primer PCR (SSP-PCR) in 204 Romanian diabetic families (756 individuals: 212 T1DM probands and 544 unaffected parents and siblings). We studied alleles transmission using the Transmission Disequilibrium Test (TDT). We found an increased transmission of CTLA-4 49G allele to diabetics (54.8%, p=0.11). The transmission of F (56.1%, p=0.063), a (55.7%, p=0.061) and T (51.8%, p=0.37) alleles of VDR gene to diabetics was increased but did not reach statistical significance. In conclusion we found the same increased transmission of CTLA-4 49 G allele to diabetics as previously reported. VDR FoqI F allele seems to be predisposing while TaqI T allele seems to be protective.