Frequency of fokI and taqI polymorphism of vitamin D receptor gene in Indian population and its association with 25-hydroxyvitamin D levels

BACKGROUND: The VDR protein is at the centre of the vitamin D endocrine system, a complex physiological system with substantial feedback regulatory mechanisms involved in maintaining serum calcium and 1, 25 dihydroxy vitamin D3. Variations in VDR gene are shown to have implications in several diseases and have also been implicated as an important genetic factor affecting bone mass. AIM: To determine the frequency of Fok I and Taq I variants in healthy Indian individuals and its association with 25-OH-Vitamin D levels. SETTINGS AND DESIGN: Blood samples were collected from 143 unrelated normal individuals (Male-84 and Female-59) and their genotypes determined. MATERIALS AND METHODS: After amplification by polymerase chain reaction, each polymorphism was genotyped by restriction fragment length polymorphism. For 100 normal healthy individuals 25-hydroxyvitamin D estimation was done using DiaSorin kit method. STATISTICAL ANALYSIS: Graph pad software was used to calculate the P values from the Chi-square. RESULTS: Out of 143 samples analyzed for FokI and TaqI polymorphisms the following genotypic frequency was obtained FF 59%, Ff 36%, ff 5% and TT 49%, Tt 43%, tt 8% respectively. CONCLUSIONS: Results indicate that the distribution of the polymorphic loci Fok I and Taq I vary considerably not only in different populations, but also within India. Furthermore, when the genotypes were analyzed with respect to 25-OH-Vitamin D levels, a significant association was seen for the Taq 1 SNP but not with the Fok I.

[3] The gene encoding the VDR is located on chromosome 12cen-q12, [4] contains 11 exons, [5] and spans approximately 75 kilobases of genomic DNA. [6]VDR gene has also been suggested as one of the candidate genes for genetic control of bone mass.Allelic variants of the gene encoding VDR, recognized by ApaI (allele A/a), BsmI (allele B/b), FokI (allele F/f) and TaqI (allele T/t) restriction endonucleases, have been associated with Bone Mass Density (BMD) [7][8][9][10] in many studies as well as with bone loss in elderly subjects [11,12] and gain after 1, 25-dihydroxy Vitamin D3 treatment.The FokI polymorphism is a T/C transition polymorphism (ATG to ACG) at the first of two potential translation initiation sites in exon II [13] has been defined using the FokI restriction endonuclease. [14]e TaqI polymorphism is a T/C nucleotide substitution (ATT to ATC) leading to a synonymous change at codon 352 (isoleucine) in exon IX [15] Bsm I [8] and ApaI [16] restriction site polymorphisms occur in the intron separating exons VIII and IX.A strong concordance exists between the absence of the BsmI (B allele) and presence of the TaqI (t allele) sites, [8] and these sites show significant linkage disequilibrium with the ApaI polymorphism.However, the agreement on this relationship is not universal.The discrepancies between studies addressing genetic risks may be attributed to genetic heterogeneity, population admixture and

Introduction
Vitamin D, is an important dietary factor that mediates its action in the body through Vitamin D receptor (VDR), a member of nuclear hormone receptor super family that from India are few and hence, in this study we present the frequency of FokI and TaqI polymorphisms in normal healthy Indian population and their association with the 25-OH-Vitamin D levels.

Subjects
Blood samples were collected from 143 unrelated normal individuals (Male-84 and Female-59) with informed consent.Individuals included were healthy adults between 25-60 years of age presenting for routine health checkup.The individuals had to fill up a detailed questionnaire regarding, medical history, with specific emphasis on fractures and as well as any family history of the same.
Blood specimens were collected after an overnight fast of 12 hours by veni-puncture using the vacutainer system from Becton Dickinson (Franklin Lakes, NJ, USA) in the anti-coagulant EDTA as well as plain bulb for serum.

DNA extraction
The genomic DNA was isolated from peripheral blood using QIAamp ® DNA Blood Mini Kit (Qiagen, Hilden, Germany).DNA yield and purity was determined by measuring absorbance at 260/280 nm.

Polymerase chain reaction
Reaction mixtures of 50 ml were used in PCR for the VDR gene (FokI, TaqI) polymorphism and DNA samples were amplified in MJ Research Peltier Thermal Cycler (PTC-200).Gels were visualized under UV transilluminator imaging system.The primers used were as reported earlier for FokI [19] and for TaqI. [20]

FokI polymorphism
DNA samples were amplified with cycling parameters as follows: Initial denaturation at 94°C for 5 minutes followed by 32 cycle of 94°C for 45 seconds, 58°C for 45 seconds, followed by 72°C for 45 seconds,

TaqI polymorphism
The PCR conditions were -initial denaturation at 94°C for six minutes followed by 35 cycle of 94°C for 45 seconds, 63°C for 60 seconds, followed by 72°C for 75 seconds, and a final extension at 72°C for seven minutes.A P value , 0.05 is considered significant for the data at 5% level of significance.3] and TaqI [Table 4] frequencies of different populations, including previous study from India with the present study by using x 2 test, a significant difference was observed.

Upon comparison of FokI [Table
In addition to this, we have also tried to correlate levels of vitamin D 3 with FokI and TaqI genotypes.5].

Discussion
Vitamin D function mediates its effects via the VDR which is a potent regulator of bone and calcium homeostasis as well as in immunomodulation, cellular differentiation and replication in different target tissues.
VDR gene polymorphisms have been associated with multiple traits and disease phenotypes like primary hyperparathyroidism, Grave's disease, Type I-diabetes mellitus and osteoporosis.

P values #
French [31] 189 33 49 18 13.210.0014 Japanese [32] 488 77 22 1 68.182 0.0001 Chinese [33] 144 90 10 0 59.23 0.0001 North Indians [22] 346 36 44 20 14.65 0.0007 Present study 143 48.9 44.3 7.6 Each population has been compared w.r.t. the Indian population and the Chi-square and P values calculated.$ :-x 2 tabulated at 5% level of significance (i.e.0.05) and 2 degrees of freedom.# :-P values have been calculated from x 2 using Graph Pad Prism software in our study.The frequency of the polymorphisms is dependent on ethnicity, hence when these frequencies were compared using chi-square with other populations the analysis was found to be statistically significant for FokI and TaqI.[Tables 3 and 4].The frequency of these polymorphisms not only vary between our population and Caucasians, but also vary from other Asian countries like Japan [21] (FF-37%, Ff-51%, ff-12% and TT-77%, Tt-22%, tt-1% respectively).The frequency of the FokI and TaqI genotypes in the present study also shows different results than that of a study conducted in North Indian population (FF-44%, Ff-49%, ff-7% and TT-49%, Tt-40%, tt-11% respectively). [22]Most data indicate that the F allele is more effective than the f allele in trans-activation of the 1, 25(OH)2-D3 signal. [23,24]Indians have lower bone density as compared to the North American and European counterparts, [25][26][27] and differences in the frequency of genetic variants may be a contributing factor.Thus the current data signifies an impact of ethnicity and provides a basis for future epidemiological and clinical studies.
Another important aspect of the study was the correlation between FokI, TaqI SNP's and 25-OH-vitamin D levels [Table 5].The TaqI SNP showed a strong correlation with respect to the Vitamin D 3 levels (P 5 0.021) whereas no correlation was observed with respect to FokI SNP (P .0.05) upon chi-square test analysis.The TaqI SNP is reported to be in linkage disequilibrium with BsmI and ApaI and can be considered as a marker for bone mineral density in individuals.Bone density was observed to be higher in some [28] but not all studies [29] in subjects with the bbaaTT haplotype than in those with BBAAtt haplotype

Conclusion
We have determined the frequency of FokI and TaqI polymorphism in the VDR gene in the Indian population.
Also, there is association of the Taq1 genotypes with the Vitamin D3 levels.

For
100 normal healthy individuals 25-hydroxyvitamin D estimation was done using DiaSorin kit method (DiaSorin, Stillwater, Minnesota USA) The DiaSorin 25-OH-D estimation consists of a two-step procedure, the first one involves a rapid extraction of 25-OH-D and other hydroxylated metabolites from serum with acetonitrile.Treated sample is then assayed using an equilibrium RIA procedure.The RIA method is based on an antibody with specificity to 25-OH-D.
and a final extension at 72°C for 7 minutes.The reaction mixture consisted of 100-200 ng genomic DNA, 200 mM each of dATP, dCTP, dGTP, dTTP (Sigma, USA), 5 ml of 10 X PCR Buffer, 0.3 ml of 1.5 U of Taq DNA Polymerase (Sigma, Missouri, USA), 20 pM of each primer (Sigma, Missouri, USA).Following amplification, the translation initiation site of the VDR gene was detected by RFLP (Restriction Fragment Length Polymorphism) using the restriction endonuclease Fok1 (New England Biolabs) at 37°C for 4 hours.Digested restriction fragments were separated on 2.5% (w/v) agarose (Sigma) gels.Bands were visualized on an UV Transilluminator Imaging system.Depending on the digestion pattern, genotypes were assigned as follows: FF homozygous for the absence of the FokI site with an undigested 265 bp band; ff homozygous for the presence of the FokI site with complete digestion into 169 bp and 96 bp bands and Ff in case of heterozygosity all three bands (265 bp, 169 bp and 96 bp) were observed [Figure 1].

Following
amplification the site on VDR gene was detected by RFLP (Restriction Fragment Length Polymorphism) using the restriction endonuclease Taq1 (GENEI, Banglore, INDIA) at 65°C for four hours.Digested restriction fragments were separated on 2.5% (w/v) agarose (Sigma) gels.Bands were visualized on an UV Transilluminator Imaging system.Genotypes were assigned as follows: TT homozygous for the absence of TaqI site 340 bp only; tt homozygous for the presence of TaqI site 293 bp and 47 bp, in case of heterozygosity Tt, all three bands (340 bp, 293 bp and 47 bp) were exhibited [Figure 2].Sequencing Genotyping of 10% of samples was confirmed by sequencing [Figure 3a and b].Amplified products were purified using QIAquick PCR purification kit (Qiagen, Hilden, Germany) and directly sequenced to identify the polymorphic site by Automated ABI prism 3100 Avant Genetic Analyzer (Applied Biosystems Inc., Foster city, Calif.) using ABI prism BigDye terminator kit (version 3.1).Statistical analysisAllele frequency was calculated as the number of occurrences of the test allele in the population divided by the total number of alleles.Hardy Weinberg Equilibrium was also applied to the allelic frequencies.Chi-square test was applied to compare the allelic frequency of different populations of the present study with different populations.The Chi-square test was also performed for comparison based on gender and finally also for correlation of 1, 25-dihydroxy vitamin D3 levels with the polymorphisms.Graph pad software was used to calculate the P values from the Chi-square.

25 -
hydroxyvitamin D levels were analyzed for 100 individuals, who were segregated into low vitamin D and those falling under the normal range (9-37.6 ng/ ml).Out of 100 subjects, 34 had low vitamin D and the remaining 66 were within the normal range.No correlation was observed with respect to the FokI SNP (P value .0.05 i.e.0.954), but the TaqI SNP showed a strong correlation with the 25-OH-vitamin D levels (P value , 0.05 i.e 0.021) [Table

(
The VDR alleles were classified according to the presence (b, t, a) or absence (B, T, A) of the BsmI, TaqI and ApaI restriction enzyme cutting sites).The possible explanation for association of the Taq1 genotype with Vitamin D levels could be that polymorphisms in the VDR gene are known to influence calcium metabolism, which in turn plays an important role in feedback mechanism of Vitamin D levels.Alternatively it is also possible that the TaqI polymorphism may be in linkage dis-equilibruim with another marker that may be the true causative factor influencing the Vitamin D levels.