Characterization of the bell polymorphism in the glucocorticoid receptor gene.
Several polymorphisms of the GR gene, which might have an impact on GC sensitivity, have been reported (6-8). Among these, the BclI polymorphism was identified by Southern blotting using human GR cDNA-specific probes (9) that identified two alleles with fragment lengths of 4.5 and 2.3 kb. Several clinical investigations have subsequently suggested that this GR polymorphism is linked to altered GR function (6,10-15). An association between the Bell polymorphism and changes in tissue-specific corticosteroid sensitivity, as well as with poor feedback regulation of the hypothalamic-pituitary-adrenal axis, has been reported (6,10). This was further documented by association of the Bell polymorphism with abdominal obesity (11, 12), insulin resistance (6,13), and development of an atherogenic profile (6,14). Similarly, the larger allele of BclI is more frequent in a group of individuals genetically predisposed to develop hypertension (15). The molecular identity of this polymorphism, however, is still unclear, and its analysis has been based on the laborious and time-consuming Southern blot approach, which requires large quantities of DNA and is difficult to apply to large-scale genotyping (6,10-15).
Here we present the characterization of the Bell polymorphism, as well as the application of two simple genotyping assays for its detection: PCR with restriction fragment length polymorphism (RFLP) analysis and allele-specific oligonucleotide (ASO) hybridization. Using these approaches, we assessed the frequency of this polymorphism in populations of different origin.
The BclI site was suggested to be situated in either the first or second intron of the GR gene (6). To search for BclI sites in these gene segments, we used the genomic sequence derived from human chromosome 5 contig (GenBank accession no. NT 029289), on which the exon/ intron boundaries were positioned according to the GR mRNA sequence information (GenBank accession no. NM_000176.1) and BLAST search (http://www.ncbi.nhn. nih.gov/BLAST/). The genomic sequence corresponding to the first two introns was analyzed for BclI restriction sites using WebCutter 2.0 software (http://www. firstmarket.com/cutter/cut2.html). We found three BclI sites, one in intron 1 and two in intron 2, whose relative positions to the exon 2/intron 2 boundary are indicated in Fig. 1A. Only the polymorphic BclI site in intron 2, 647 by from exon/intron junction, produced the fragment sizes corresponding to those obtained by Southern blot experiments (i.e., fragments of 2.2 kb generated in the presence and 3.9 kb in the absence of the Bc1I site; Fig. 1A). Although the size of the larger allele would be slightly different from that reported previously (9), no other BclI site produced a fragment of similar size.
[FIGURE 1 OMITTED]
Using this information, we designed primers flanking the Bc1I site at position +647 (forward, 5'-AAATTGAAGCTTAACAATTTTGGC-3'; reverse, 5'-GCAGTGAACAGTGTACCAGACC-3') and amplified genomic DNA samples from the Institutional DNA bank of healthy volunteers recruited for the study of human genomic sequences variability. (The study was approved by the Institutional Ethical Committee, and informed consent was obtained from all participating individuals.) The PCR 206-bp product was amplified in 20 [micro]L containing 20 ng of genomic DNA, 0.5 [micro]M each amplimer, 100[micro]M deoxynucleotide triphosphates, 10 mM Tris-HCl (pH 8.3), 1.5 mM Mg[Cl.sub.2], 50 mM KCl, and 0.5 U of Taq polymerase (Platinum; Invitrogen) with the following conditions: initial denaturation at 94[degrees]C for 5 min; 40 cycles of denaturation at 94[degrees]C for 30 s, annealing at 59[degrees]C for 30 s, and extension at 72[degrees]C for 45 s; followed by a final extension at 72[degrees]C for 7 min.
To confirm the presence of the BclI polymorphism, we digested 10 [micro]L of the PCR products with 4 U of BclI (New England BioLabs) for 6 h at 50[degrees]C and separated the resulting digested fragments on a 3% agarose gel. Digestion of the PCR product gave the following predicted fragment sizes: 90 and 116 by in the case of homozygotes for the smaller allele, an additional band of 206 by for heterozygous individuals, and a single band of 206 by for larger allele homozygotes (Fig. 1B). To characterize the underlying base substitution of the BclI polymorphism, we directly sequenced the PCR product using the Thermo Sequenase[TM] Radiolabeled Terminator Cycle Sequencing Kit (USB Corporation) according to the manufacturer's instructions. We found a G-to-C transition in the second intron, 646 by from the exon 2/intron 2 junction (Fig. 1C), that abolished the Bc1I restriction site (TGATCA to TGATCA, where the underlined bases indicate the transition), thus producing the larger allele. Similar efforts to replace Southern blot analysis by PCR-based methods in analysis of different polymorphisms have been reported in the literature (16,17).
The identification of the underlying base substitution allowed us to apply a PCR-ASO genotyping assay that, in addition to PCR-RFLP, has been widely used to analyze gene mutations and variations in numerous genes (18). We previously reported the successful use of this approach for large-scale genotyping (19). For this method, PCR products were denatured in 0.33 mol/L NaOH and 16.5 mmol/L EDTA in a total volume of 200 [micro]L and subsequently transferred, in duplicate, to a HYBOND-n+ membrane (Amersham Pharmacia Biotech) and cross-linked to the membrane by use of ultraviolet light. Blots were prehybridized for 30 min at 37[degrees]C in 10 mL of a solution containing 1x saline-sodium phosphate-EDTA (SSPE; 150 mmol/L NaCl, 10 mmol/L Na[H.sub.2]P[O.sub.4], 1.1 mmol/L EDTA, pH 7.4), 0.75 mol/L NaCl, 70 mmol/L Tris-HCl, pH 7.4), 10 g/L sodium dodecyl sulfate, and 200 mg/L heparin. ASO probes (50 pmoles) were 5'-labeled using [[gamma]-[sup.32]P]ATP (6000 Ci/mmol) and T4 kinase (Life Technologies) to a specific activity of 1-3 x [10.sup.6] cpm/ pmol. Hybridization with the 5 pmol of ASO-specific probe was carried out for 30 min at 42[degrees]C in an excess (10x) of the nonlabeled probe for the other variant allele of the same polymorphism. The membranes were then washed with 2x SSPE containing 1 g/L sodium dodecyl sulfate for 10 min at room temperature and exposed overnight at -80[degrees]C with intensifying screens. Identical twin membranes were hybridized with the allelic probes specific for the G (gag att Gat cag cag) or C (gag att Cat cag cag) variant of the BclI polymorphism and read in parallel. DNA samples of known genotypes served as controls. Representative examples of genotypes obtained by the ASO approach are presented in Fig. 1D.
Using these two genotyping assays, we analyzed DNA samples of individuals from several populations, including Africans, Asians (both Southeast and East Asia), Amerindians, Middle Easterners, and Europeans. Both methods generated concordant results, thus validating the usefulness of both assays. The number of individuals with different genotypes, as well as the frequency of allele C in the tested populations, is given in Table 1; the highest frequency of allele C was observed in Asians [mean (SD), 32.8 (8.7)%], and the lowest was in Amerindians [15.2 (6.2)%]. The frequency observed here for Europeans was similar to the one reported for the larger allele in Sweden (6).
We conclude that characterization of the Bc1I polymorphism, together with the availability of PCR-based genotyping approaches, could allow fast screening of this polymorphism for monitoring of both disease susceptibility and therapeutic response variability. Further studies clarifying the reason for an association of this polymorphism with altered GR function could provide additional insight into the variability of the GR locus and the role of the BclI polymorphism.
This work was supported by the Cancer Research Society, Inc. and the Centre de Recherche, Hopital Ste-Justine. I.F. has a studentship and M.K. and D.S. have scholarships from the Fonds de la Recherche en Sante du Quebec. We are grateful to Alan Lovell for critical reading of the manuscript.
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Isabelle Fleury,  Patrick Beaulieu,  Melanie Primeau,  Damian Labuda, [1,2] Daniel Sinnett, [1,2] and Maja Krajinovic [1,2] * ( Service d'Hematologie-Oncologie, Centre de Recherche, Hopital Sainte-Justine, Montreal (Quebec), H3T 1C5 Canada;  Departement de Pediatrie, Universite de Montreal, Montreal (Quebec), H3T 1C5 Canada; * address correspondence to this author at: Centre de Recherche, Hopital Sainte-Justine, 3175 Cote Ste-Catherine, Montreal (Quebec), H3T 1C5 Canada; fax 514-345-4731, e-mail email@example.com)
Table 1. Allele and genotype frequencies of the BclI polymorphism in the GR gene among different populations. (a) African Amerindian European No. of individuals 42 33 38 Genotype, n (%) GG 27 (64%) 23 (70%) 18 (47%) GC 13 (31%) 10 (30%) 18 (47%) CC 2 (5%) 0 (0%) 2 (5%) Mean (SD) frequency 20.2 (6.2) 15.2 (6.2) 28.9 (7.4) of allele C, % Asian Middle Eastern No. of individuals 29 36 Genotype, n (%) GG 12 (41%) 24 (67%) GC 15 (52%) 12 (33%) CC 2 (7%) 0 (0%) Mean (SD) frequency 32.8 (8.7) 16.7 (6.2) of allele C, % (a) Genotyping was performed using both the PCR-RFLP and PCR-ASO assays.
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|Title Annotation:||Technical Briefs|
|Author:||Fleury, Isabelle; Beaulieu, Patrick; Primeau, Melanie; Labuda, Damian; Sinnett, Daniel; Krajinovic,|
|Date:||Sep 1, 2003|
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