Whole genome analysis on the genetic backgrounds associated with the secondary failure to etanercept in patients with rheumatoid arthritis.

OBJECTIVES: Etanercept is effective for the treatment of rheumatoid arthritis (RA). However, some of the patients eventually lose efficacy (secondary failure) despite the absence of neutralizing antibodies. We aimed to explore single nucleotide polymorphisms (SNPs) associated with secondary failure. METHODS: We recruited RA patients given etanercept at 50 mg/week for ≥6 months from the Matsubara Mayflower Hospital RA registry. They were assigned to responders, secondary failure patients, and non-responders according to Disease Activity Score. Genome-wide association study (GWAS) was performed using Illumina HumanHAP300k BeadChips and the results were analyzed with Plink software. Clinical backgrounds were compared by ANOVA and contingency table analysis. The protocol was approved by IRB and written informed consent was obtained. RESULTS: Ninety, 27 and 17 patients were assigned to responders, secondary failure patients, and non-responders, respectively. No significant differences were observed regarding clinical backgrounds among the groups. GWAS revealed that six and 37 SNPs may be associated with secondary failure to etanercept with p< 10-6 and <10-5, respectively. CONCLUSION: While our preliminary results with borderline significance should be validated by studies with a greater population size, some of the SNPs detected by our GWAS may be involved in the development of secondary failure to etanercept.

Identification of an IgE-binding epitope of a major buckwheat allergen, BWp16, by SPOTs assay and mimotope screening.

BACKGROUND: The buckwheat 16-kDa protein (BWp16), as reported in our previous study, is a major allergen in buckwheat; however, the IgE-binding epitopes of BWp16 have not as yet been identified. METHODS: We screened candidates for IgE-binding epitopes on BWp16 by using arrays of overlapping peptides synthesized on activated cellulose membranes (SPOTs membrane). The mimotope method was also used to analyze IgE-binding epitopes of BWp16. Nine single alanine (Ala) mutants of BWp16 expressed in Escherichia coli were used to confirm the epitopes of BWp16. The IgE-binding activity of single Ala mutants of BWp16 was determined by ELISA with mouse anti-BWp16 polyclonal antiserum or ELISA inhibition with sera from buckwheat allergic patients. RESULTS: The SPOTs assay identified amino acid residues 99-110, i.e. EGVRDLKELPSK, as a candidate for the linear IgE-binding epitope of BWp16. The mimotope method indicated that peptides similar to EGVRDLKE were candidate sequences for epitopes of BWp16. Ala scanning of rBWp16 revealed that all EGVRDLKE peptides containing a single amino acid mutation had weaker IgE-binding activity than rBWp16 WT. An ELISA inhibition assay for rBWp16 WT revealed the inhibitory effect of rBWp16 D103A to be less than that of rBWp16 WT. CONCLUSIONS: We identified the peptide EGVRDLKE as a very likely candidate for the IgE-binding epitope of BWp16, and Asp103 as the critical amino acid in BWp16. This is the first report on the identification of IgE-binding epitopes of BWp16. Our findings will contribute to the production of BWp16 hypoallergens, and to allergen-specific immunotherapy for buckwheat allergy.

Confirmation of a predicted lack of IgE binding to Cry3Bb1 from genetically modified (GM) crops.

Some GM crops including MON863 corn and stack varieties contain Cry3Bb1 protein. Cry3Bb1 is very important from the standpoint of assessing the safety of GM crops. In this study Cry3Bb1 was assessed from the standpoint of possible binding to IgE from allergy patients. First, an ELISA that was improved in our laboratory was used to test serum samples from 13 corn allergy patients in the United States with recombinant Cry3Bb1 expressed in Escherichia coli, and serum samples from 55 patients in Japan with various food allergies were also assayed. Two samples from the Japanese allergy patients were suspected of being positive, but Western blotting analysis with purified Cry3Bb1 indicated that the binding between IgE and Cry3Bb1 was nonspecific. Ultimately, no specific binding between IgE and recombinant Cry3Bb1 was detected. Next, all proteins extracted from MON863 corn and non-GM corn were probed with IgE antibodies in serum samples from the corn allergy patients by Western blotting, but the staining patterns of MON863 and non-GM corn were similar, meaning that unintended allergic reactions to MON863 are unlikely to occur. Our study provides additional information that confirms the predicted lack of IgE binding to Cry3Bb1 in people with existing food allergies.

Efficacy of tocilizumab and evaluation of clinical remission as determined by CDAI and MMP-3 level.

Tocilizumab, a biological agent developed in Japan, is a human anti-interleukin-6 (anti-IL-6) receptor antibody. Rheumatoid arthritis improves with its use. A remission rate of 59% is attainable, as measured by disease activity score 28 (DAS28) in the SAMURAI study. However, in tocilizumab treatment, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) levels drop to negative values; therefore we sought to utilize a different index for measuring its efficacy. In order to evaluate the effects of tocilizumab we carried out this study using clinical disease activity index (CDAI), as it is not reliant on blood data and would also allow us to determine which markers are present in remission. Twenty-two patients under treatment with tocilizumab participated in this study. Effects of treatment as well as the remission rate were measured by CDAI and DAS28 3 months after initiation of treatment. IL-6 and matrix metalloproteinase-3 (MMP-3) levels were measured at the same time. We studied the clinical efficacy of tocilizumab using DAS28 after treatment; remission as measured by DAS28 was 57.1% at 1 year. However, the remission rate as measured by CDAI was only 19.1% at 1 year. CDAI was not only correlated with DAS28, but also other clinical variables, MMP-3, and IL-6. We conclude that CDAI is effective in measuring clinical response to tocilizumab treatment, and that MMP-3 level is as useful as IL-6 level as an indicator.

JNK-binding protein 1 regulates NF-kappaB activation through TRAF2 and TAK1.

The mitogen-activated protein kinase (MAPK) cascades, including c-Jun N-terminal kinase (JNK), are composed of a MAPK, MAPK kinase (MAPKK), and MAPKK kinase (MAPKKK). Previously, we reported that JNK-binding protein 1 (JNKBP1) enhances JNK activation induced by the TGF-beta-activated kinase1 (TAK1) MAPKKK in transfected cells. We have investigated whether JNKBP1 functions as an adaptor protein for nuclear factor (NF)-kappaB activation mediated by TAK1 in COS-7 cells. Co-expression experiments showed that JNKBP1 interacted with not only TAK1, but also with its upstream regulators, TNF-receptor associated factors 2 and 6 (TRAF2 and TRAF6). An endogenous interaction between JNKBP1 and TRAF2 or TAK1 was confirmed by immunoprecipitation analysis. We also found that JNKBP1 could enhance the NF-kappaB activation induced by TAK1 and TRAF2, and could promote TRAF2 polyubiquitination. These results suggest a scaffolding role for JNKBP1 in the TRAF2-TAK1-NF-kappaB signaling pathway.

[Characterization of anti-mouse prion peptide single chain Fv antibody by phage display].

Antibodies can distinguish not only differences in amino acid sequences (primary structure), but also differences in three-dimensional structure and thus may be useful for detecting the conversion of prion proteins, especially in vivo. For diagnosis, we prepared chicken single chain variable fragment (scFv) antibodies that specifically recognized a prion protein using a phage display approach. As antigen, mouse prion protein (MoPrP) 138-153 containing YYR residues was conjugated with KLH. Total RNA was extracted from the splenocytes of an immunized chicken, and the cDNA of scFv was ligated in a phagemid vector. The phage display scFv library was panned against the peptide antigen four times. Twenty-three scFv phage clones that tested positive using ELISA with the peptide antigen were then reacted with recombinant mouse prion protein (23-231), mouse brain homogenate, mouse neuroblastoma Neuro-2a, recombinant human V129 and M129 prion proteins, and human glyoma T98G using ELISA, immunoblotting analysis, and immunocytochemistry. The results suggested that the scFv phage clones were useful for detecting mouse and human prion proteins.

Genetic association between aldehyde dehydrogenase 2 (ALDH2) variation and high-density lipoprotein cholesterol (HDL-C) among non-drinkers in two large population samples in Japan.

AIM: Moderate alcohol consumption appears to confer some protection against coronary heart disease, which is related to an increase in high-density lipoprotein cholesterol (HDL-C). The genotype of aldehyde dehydrogenase 2 (ALDH2) is closely related to alcohol metabolism but a relationship between ALDH2 genotypes and HDL-C levels has not been proven. We undertook a large-scale correlation study between HDL-C levels and ALDH2 genotype among Japanese non-drinkers to investigate the possibility that HDL-C levels could be associated with ALDH2 genotype. METHODS: We examined a population-based sample of Japanese subjects who do not consume alcohol (n=1,736) to investigate the relationship between ALDH2 genotypes and lipid or lipoprotein concentrations in serum. We also investigated whether an association between ALDH2 genotype and HDL-C levels might be found in another Japanese sample. RESULTS: In an independent population of non-drinkers from a different geographical region of Japan, HDL-C levels were associated with the same ALDH2 genotypes. CONCLUSIONS: The results of the present study suggested that genetic variation in the ALDH2 gene can influence HDL-C levels, independent of alcohol consumption.

Immunological characterization and mutational analysis of the recombinant protein BWp16, a major allergen in buckwheat.

Buckwheat allergy is one of the most critical diseases manifested by severe and dangerous symptoms in Japan and other countries. We previously isolated the cDNA encoding protein BWp16, a member of the 2S albumin family with a conserved motif of 8 cysteine (Cys) residues. Comparison of the deduced amino acid sequences of BWp16 and related proteins in the 2S albumin family showed similarities between BWp16 and BW 8-kDa from buckwheat, Ara h 6 from peanuts and Ric c 1 from castor bean. Purified recombinant BWp16 (rBWp16) expressed in Escherichia coli was recognized by >80% of sera from patients with positive for IgE binding to buckwheat. Mutational analysis of rBWp16 revealed that 7 out of 10 mutants in the Cys residues showed weaker IgE binding to patient's serum than wild-type rBWp16 (rBWp16 WT). Mutations of Cys65 and Cys66 in rBWp16 decreased the pepsin digestibility of the protein, and an ELISA inhibition assay revealed a weaker inhibitory effect of rBWp16 C65S than that of rBWp16 WT. These results suggest that the Cys residues, especially Cys65, are involved in the allergenicity of rBWp16. Our findings provide new evidence for the role of Cys residues in 2S albumin family proteins and open the door to the production of hypoallergens and application to safe diagnostic methods and allergen-specific immunotherapy of buckwheat allergy.

Common null variant, Arg192Stop, in a G-protein coupled receptor, olfactory receptor 1B1, associated with decreased serum cholinesterase activity.

AIM: Non-functioning single nucleotide polymorphisms (nSNPs) that result in premature termination codons, that is null-alleles of the respective genes, may have phenotypic effects on clinical parameters. We conducted association studies involving several G-protein coupled receptors (GPCRs) that harbor nSNPs, using clinical parameters of liver function in a general population consisting of 2969 Japanese adults. METHODS: SNP typings were performed with TaqMan and Invader assays. Quantitative associations between genotypes and clinical parameters were analyzed by analysis of variance. Linkage disequilibrium (LD) was tested by Haploview Version 3.3. Haplotype-based association was performed using the haplo.stats program. RESULTS: A significant correlation (P = 0.0057) was identified between serum cholinesterase activity (CHE) and an nSNP (Arg192Stop) in the olfactory receptor (OR) 1B1 gene, a member of the GPCR gene family. This nSNP was associated with decreased serum CHE (P = 0.0013). LD analysis based on eight selected SNPs at the locus revealed three LD blocks. The Arg192Stop nSNP was located on the second LD block, which covered one-third of the 3'-portion of the gene. CONCLUSION: These results suggested that the null-allele of OR1B1 might affect metabolism of serum cholinesterase in carriers of this nSNP.

Association of an intronic haplotype of the LIPC gene with hyperalphalipoproteinemia in two independent populations.

Hepatic lipase (HL) plays a major role in the regulation of plasma lipids. Several groups seeking to find association between the gene encoding HL (LIPC) and plasma concentrations of high-density lipoprotein cholesterol (HDLc) using various methods and populations have reported conflicting results. We have approached the problem of demonstrating a relationship between the LIPC locus and HDLc by means of haplotype association using four single nucleotide polymorphisms (SNPs) (rs12594375G/A, rs8023503C/T, rs4775047C/T, and rs11634134T/A) located in intron 1 of the LIPC gene in two independent Japanese populations consisting of 2,970 and 1,638 individuals, respectively. Significant association between hyperalphalipoproteinemia and a specific haplotype in this intron was detected in both populations. When HDLc levels among the three haplotypic categories were analyzed [haplotype rs8023503C/rs12594375G (haplotype-1; H1) homozygotes (H1H1), haplotype rs8023503T/rs12594375A (haplotype-2; H2) homozygotes (H2H2), and heterozygotes (H1H2)], HDLc levels were lowest among H1H1 [mean +/- standard error (SE) = 58.4 +/- 0.4 mg/dl], highest among H2H2 (62.5 +/- 0.8 mg/dl), and intermediate among H1H2 (59.2 +/- 0.4 mg/dl) (P = 0.00011), indicating that H2 haplotype elevates plasma HDLc levels. This association was validated in the second population (n = 1,638) (P = 0.00070). The results provide convincing evidence that the LIPC locus influences HDL metabolism.

A nonfunctioning single nucleotide polymorphism in olfactory receptor gene family is associated with the forced expiratory volume in the first second/the forced vital capacity values of pulmonary function test in a Japanese population.

The forced expiratory volume in the first second (FEV1.0)/the forced vital capacity (FVC) is an important index of a single forced expiration. Ectopic expression of the human olfactory receptor (OR) gene family in the lungs has suggested its potential involvement of respiratory physiology. We hypothesized that the individual variability of FEV1.0/FVC value may be attributed to the genetic variance of the OR gene family caused by the nonfunctioning SNPs (nSNPs). We conducted quantitative trait locus (QTL) analyses of population having the 7 OR gene nSNPs and FEV1.0/FVC values by ANOVA, in 2970 samples in the Yamagata Takahata cohort. We found significant association of one nSNP [rs10838851, OR, family 4, subfamily X, member 1 (OR4X1) gene, Tyr273Ter*] with FEV1.0/FVC (%) (P = 0.008). The FEV1.0/FVC value (%) of population having OR4X1 gene nSNP Ter*/Ter*, Ter*/Tyr, and Tyr/Tyr were 78.9 +/- 0.2, 78.2 +/- 0.2, and 77.7 +/- 0.4, respectively. Haplotype-based analysis of the OR4X1 gene with FEV1.0/FVC values demonstrated that two exclusive haplotypes [Hap-1/Hap-2 (frequency 0.669/0.330): SNP1 (rs7106648)T/A-SNP2 (rs871249)G/A-SNP3 (rs713325)G/A-SNP4 (rs10838851)A (Ter*)/T (Tyr)-SNP5 (rs4752923)G/A-SNP6 (rs960640)G/A] were significantly associated with FEV1.0/FVC values (global P = 0.005). These results suggest that OR4X1 may be one of the genes that contribute to the individual variability of FEV1.0/FVC value in pulmonary function test.

Molecular cloning of cDNA, recombinant protein expression and characterization of a buckwheat 16-kDa major allergen.

BACKGROUND: Buckwheat is a common food in Japan, Korea and other countries. A candidate major buckwheat allergen, a 16-kDa protein (BWp16), was previously characterized as a pepsin-resistant protein associated with immediate-type allergies to buckwheat. However, whether recombinant BWp16 can react with a patient's IgE remains uncertain. METHODS: The cDNA encoding BWp16 from Japanese buckwheat seeds was cloned based on the sequences obtained by the 5'-rapid amplification of cDNA ends (RACE) and 3'-RACE PCR. Recombinant BWp16 protein expressed in Escherichia coli was purified using affinity chromatography. Western blotting, ELISA and cross inhibition tests of the purified recombinant BWp16 were performed using sera from patients with positive IgE binding to buckwheat and controls. Pepsin digestion experiments were also performed. RESULTS: The full-length cDNA encodes 149 amino acid residues with a calculated molecular mass of 16.9 kDa. The deduced amino acid sequence included a putative signal peptide sequence. BWp16 showed significant homologies to the buckwheat 8-kDa allergen and Ricinus communis (castor bean) 2S albumin. Sera from patients with positive IgE binding to buckwheat reacted with the purified BWp16. Cross inhibition tests revealed immunological equivalence of the purified recombinant and natural BWp16. The recombinant and natural BWp16 were comparably resistant to pepsin digestion. CONCLUSIONS: BWp16 belongs to the 2S albumin family and is a buckwheat allergen. This purified recombinant BWp16 could be used in the diagnosis of buckwheat allergy.

Identification of regulatory sites in the human PXR (NR1I2) promoter region.

The human pregnane X receptor (hPXR, NR1I2) is a member of the nuclear receptor superfamily and a key regulator of genes encoding several major cytochrome P450 enzymes and transporters. However, the transcriptional regulation of hPXR itself remains unclear. We recently reported significant diversity in the 5' region of human hepatic PXR transcripts and identified the major transcription initiation site. Here, we investigate the transcriptional regulatory sites in the hPXR 5'-flanking region. Luciferase reporter constructs containing various lengths of 5'-flanking region, up to 10.5 kb upstream of the major transcription initiation site, were assessed for promoter activity in HepG2 cells. We mapped the minimal essential region for promoter activity to a 160 bp region upstream of the transcription initiation site, an area that also showed nuclear protein binding. Constructs with mutations introduced into these protein-binding sites demonstrated reduced promoter activity concomitant with reduced DNA-protein binding activity. hPXR promoter activity was observed in HepG2 cells but not in HeLa cells. Likewise, nuclear protein binding to promoter elements was also observed in HepG2 but not HeLa cells. The present study provides basic information on the transcriptional regulation of hPXR and may help elucidate the regulatory mechanisms of hPXR target genes.

5' diversity of human hepatic PXR (NR1I2) transcripts and identification of the major transcription initiation site.

The human pregnane X receptor (PXR) is a crucial regulator of the genes encoding several major cytochrome P450 enzymes and transporters, such as CYP3A4 and MDR1, but its own transcriptional regulation remains unclear. To elucidate the transcriptional mechanisms of human PXR gene, we first endeavored to identify the transcription initiation site of human PXR using 5'-RACE. Five types of 5'-variable transcripts (a, b, c, d, and e) with common exon 2 sequence were found, and comparison of these sequences with the genomic sequence suggested that their 5' diversity is derived from initiation by alternative promoters and alternative splicing. None of the exons found in our study contain any new in-frame coding regions. Newly identified introns IVS-a and IVS-b were found to have CT-AC splice sites that do not follow the GT-AG rule of conventional donor and acceptor splice sites. Of the five types of 5' variable transcripts identified, RT-PCR showed that type-a was the major transcript type. Four transcription initiation sites (A-D) for type-a transcript were identified by 5'-RACE using GeneRacer RACE Ready cDNA (human liver) constructed by the oligo-capping method. Putative TATA boxes were located approximately 30 bp upstream from the transcriptional start sites of the major transcript (C) and the longest minor transcript (A) expressed in the human liver. These results indicate that the initiation of transcription of human PXR is more complex than previously reported.

Functional analysis of six human aryl hydrocarbon receptor variants in a Japanese population.

Aryl hydrocarbon receptor (AhR) is an important transcriptional regulator involved in the induction of CYP1A1, CYP1A2, CYP1B1, UGT1A1, and UGT1A6. In this study, functional properties of four novel naturally occurring human AhR variants (K401R, N487D, I514T, and K17T/R554K) were examined along with the single variants K17T and R554K. The luciferase reporter assay using the CYP1A1 promoter reporter in HeLa cells treated with beta-naphthoflavone or 3-methylcholanthrene, which are known as typical agonists for AhR, showed that reporter activities of the K401R and N487D variants were reduced to 40 to 58% of those of wild-type (WT) but not of the other variants. Similarly, the K401R and N487D variants also reduced the omeprazole-induced reporter activities to approximately 56 and 74% of those of the WT, respectively. The reduced activities of the two variants were probably caused by the reduced protein expression levels, since the protein levels of the K401R and N487D variants were approximately 52 and 47% of the WT, respectively, without any changes in their mRNA levels. The reduced protein levels were recovered by treatment with a proteasome inhibitor MG132 [N-benzoyloxycarbonyl (Z)-Leu-Leu-leucinal], suggesting that the reduced protein levels were caused by the accelerated proteasomal degradation by a proteasome. Together, the current data demonstrate that the K401R and N487D variants reduce their apparent transcriptional activities, both ligand-induced and omeprazole-induced activation, probably through reduced protein expression. Thus, these two variants may influence drug metabolism through reduced induction of CYP1A1 and other target enzymes.

Novel genetic polymorphisms in the NR3C1 (glucocorticoid receptor) gene in a Japanese population.

Glucocorticoid receptor, encoded by NR3C1, is a transcriptional regulator of many drug metabolizing enzymes and anti-inflammatory molecules. In order to identify genetic variations of the NR3C1 gene, genomic DNA from 265 Japanese individuals was sequenced. Fifty genetic polymorphisms were identified, including 32 novel ones [3 were in coding exons, 17 in the introns, 4 in the 5'-untranslated region (UTR), and 8 in the 5'-flanking region]. The novel nonsynonymous variation was 420G>T (Lys140Asn), and the allele frequency was 0.004. We did not detect any nonsynonymous polymorphism reported previously in other races, including a relatively frequent SNP Asn363Ser found in Caucasians and African-Americans. Thus, ethnic differences between Japanese and other races are suggested to exist in NR3C1.

Functional characterization of five novel CYP2C8 variants, G171S, R186X, R186G, K247R, and K383N, found in a Japanese population.

Cytochrome P450 2C8 is one of the primary enzymes responsible for the metabolism of a wide range of drugs such as paclitaxel, cerivastatin, and amiodarone. We have sequenced the CYP2C8 gene from 201 Japanese subjects and found five novel nonsynonymous single nucleotide polymorphisms (SNPs): 511G>A (G171S), 556C>T (R186X; X represents the translational stop codon), 556C>G (R186G), 740A>G (K247R), and 1149G>T (K383N), with the allele frequency of 0.0025. The CYP2C8 variants were heterologously expressed in COS-1 cells and functionally characterized in terms of expression level, paclitaxel 6alpha-hydroxylase activity, and intracellular localization. The prematurely terminated R186X variant was undetectable by Western blotting and inactive toward paclitaxel 6alpha-hydroxylation. The G171S, K247R, and K383N variants exhibited properties similar to those of the wild-type CYP2C8. Paclitaxel 6alpha-hydroxylase activity of the R186G transfectant was only 10 to 20% that of wild-type CYP2C8. Furthermore, the R186G variant displayed a lower level of protein expression in comparison to the wild type, which was restored by the addition of a proteasome inhibitor (MG-132; Z-Leu-Leu-Leu-aldehyde). The reduced CO-difference spectral analysis using recombinant proteins from an insect cell/baculovirus system revealed that the R186G variant has a minor peak at 420 nm in addition to the characteristic Soret peak at 450 nm, suggesting the existence of improperly folded protein. These results indicate that the novel CYP2C8 SNPs, 556C>T (R186X) and 556C>G (R186G), could influence the metabolism of CYP2C8 substrates such as paclitaxel and cerivastatin.

Ethnic differences in genetic polymorphisms of CYP2D6, CYP2C19, CYP3As and MDR1/ABCB1.

Metabolic capacities for debrisoquin, sparteine, mephenytoin, nifedipine, and midazolam, which are substrates of polymorphic CYP2D6, CYP2C19, and CYP3A, have been reported to exhibit, in many cases, remarkable interindividual and ethnic differences. These ethnic differences are partly associated with genetic differences. In the case of the drug transporter ABCB1/MDR1, interindividual differences in its transporter activities toward various clinical drugs are also attributed to several ABCB1/MDR1 genetic polymorphisms. In this review, the existence and frequency of various low-activity alleles of drug metabolizing enzymes as well as populational drug metabolic capacities are compared among several different races or ethnicities. Distribution of nonsynonymous ABCB1/MDR1 SNPs and haplotype frequency in various races are summarized, with the association of nonsynonymous SNPs with large functional alterations as a rare event.

Genetic variations of the AHR gene encoding aryl hydrocarbon receptor in a Japanese population.

Aryl hydrocarbon receptor (AhR), encoded by the AHR gene, is a transcriptional factor that induces various drug metabolizing enzymes in response to diverse endogenous and exogenous ligands. In order to identify genetic variations of the AHR gene, genomic DNA from 242 Japanese individuals was sequenced. We identified 32 single nucleotide variations, including 25 novel ones [7 were in the coding exons, 7 in the introns, 1 in the 5'-untranslated region (UTR), 5 in the 3'-UTR, 2 in the 5'-flanking region, and 3 in the 3'-flanking region] and a GGGGC repeat polymorphism (a novel microsatellite marker) in the promoter region. The novel nonsynonymous variations were 50A>C (Lys17Thr), 1202A>G (Lys401Arg), 1459A>G (Asn487Asp), and 1541T>C (Ile514Thr). The allele frequencies were 0.010 for 1459A>G (Asn487Asp) and 0.002 for the other 3 variations. Also detected in this analysis was the known nonsynonymous single nucleotide polymorphism 1661G>A (Arg554Lys) at a 0.444 frequency.

Functional characterization of four naturally occurring variants of human pregnane X receptor (PXR): one variant causes dramatic loss of both DNA binding activity and the transactivation of the CYP3A4 promoter/enhancer region.

Metabolism of administered drugs is determined by expression and activity of many drug-metabolizing enzymes, such as the cytochrome P450 (P450s) family members. Pregnane X receptor (PXR) is a master transcriptional regulator of many drug/xenobiotic-metabolizing enzymes, including P450s and drug transporters. In this study, we describe the functional analysis of four naturally occurring human PXR (hPXR) variants (R98C, R148Q, R381W, and I403V) that we have recently identified. By a reporter gene assay using the CYP3A4 promoter/enhancer reporter in COS-7 or HepG2 cells, it was found that the R98C variant failed to transactivate the CYP3A4 reporter. The R381W and I403V variants also showed varying degrees of reduction in transactivation, depending on the dose of PXR activators, rifampicin, clotrimazole, and paclitaxel. The transcriptional activities of the R148Q variant were not significantly different from that of the wild-type hPXR. The electrophoretic mobility shift assay revealed that only the R98C variant lacked DNA binding. Furthermore, the cellular localization of the hPXR proteins was analyzed. All four variants as well as the wild-type hPXR localized exclusively to the nucleus, regardless of the presence or absence of rifampicin. These data suggest that the R98C, R381W, and I403V hPXR variants, especially R98C, may influence the expression of drug-metabolizing enzymes and transporters, which are transactivated by PXR.