Potential Minor Haplotypes of CYP2D6 in the Japanese Population.

BACKGROUND: CYP2D6 is one of the most significant polymorphic genes of drugmetabolizing enzymes due to its association with different metabolic activities and the pharmacokinetics of CYP2D6 substrates. OBJECTIVE: The objective of this study was to explore for a novel haplotype of CYP2D6 in the Japanese population by using a large database of previous clinical studies. METHODS: We analyzed CYP2D6 genotype data from a total of 723 Japanese individuals for 8 loci (100C>T, 1758G>A, 1846G>A, 2573 insertion of C, 2850C>T, 2988G>A, 4125 insertion of 9bp, and 4180G>C) and gene deletion. Genotypes were determined by the designated alleles CYP2D6*2, *4, *5, *10, *14A, *14B, *18, *21, and *41. RESULTS: The frequencies of the common major haplotypes CYP2D6*1, *10, and *2 in the Japanese population were respectively 43.5%, 38.0%, and 11.3%. In 11 subjects, diplotypes of CYP2D6 were not identified and the genotypes at the 8 loci suggested that there were 2 minor haplotypes, one with only a variation at 4180G>C compared with the wild type CYP2D6*1 (Hap1, frequency: 0.4%) and one with only a variation at 100C>T (Hap2, frequency: 0.4%). The Hap1 haplotype is considered to have no effect on metabolic activity, while it is estimated that the Hap2 haplotype does have an effect on metabolic activity. By comparing with the allele nomenclature for CYP2D6, the Hap2 haplotype was considered to be a potentially novel haplotype involving 100C>T without 4180G>C. CONCLUSION: Using a large database of CYP2D6 genotypes in the Japanese population, we found a novel haplotype which involves 100C>T without 4180G>C. Although the haplotype will need to be confirmed by full sequencing, it may be a unique haplotype with an exception to the strong linkage disequilibrium between 100C>T and 4180G>C.

Japan PGx Data Science Consortium Database: SNPs and HLA genotype data from 2994 Japanese healthy individuals for pharmacogenomics studies.

Japan Pharmacogenomics Data Science Consortium (JPDSC) has assembled a database for conducting pharmacogenomics (PGx) studies in Japanese subjects. The database contains the genotypes of 2.5 million single-nucleotide polymorphisms (SNPs) and 5 human leukocyte antigen loci from 2994 Japanese healthy volunteers, as well as 121 kinds of clinical information, including self-reports, physiological data, hematological data and biochemical data. In this article, the reliability of our data was evaluated by principal component analysis (PCA) and association analysis for hematological and biochemical traits by using genome-wide SNP data. PCA of the SNPs showed that all the samples were collected from the Japanese population and that the samples were separated into two major clusters by birthplace, Okinawa and other than Okinawa, as had been previously reported. Among 87 SNPs that have been reported to be associated with 18 hematological and biochemical traits in genome-wide association studies (GWAS), the associations of 56 SNPs were replicated using our data base. Statistical power simulations showed that the sample size of the JPDSC control database is large enough to detect genetic markers having a relatively strong association even when the case sample size is small. The JPDSC database will be useful as control data for conducting PGx studies to explore genetic markers to improve the safety and efficacy of drugs either during clinical development or in post-marketing.

Interaction of genetic markers associated with serum alkaline phosphatase levels in the Japanese population.

In the present genome-wide association study of 2,994 Japanese subjects, rs2071699 (35C>T) in the fucosyltransferase 1 (FUT1) gene was identified as a marker associated with serum alkaline phosphatase (ALP) levels. This gene encodes α(1,2)-fucosyltransferase, which is responsible for the synthesis of H antigens. In a linear regression model incorporating genetic markers, rs550057 (C>T), which is located within an intron of the ABO blood group (ABO) locus, rs2071699 in FUT1 and a gene-gene interaction between these loci accounted for 12.4, 0.9 and 0.3% of the total variability in the serum ALP level, respectively. Further association analysis using imputed genotypes detected rs1047781 in FUT2. rs1047781 is well known in this association with serum ALP levels and showed a moderate linkage with rs2071699 in FUT1. An interaction analysis using rs1047781 in FUT2 also suggested that the interaction with rs550057 in ABO is significant and contributes to the interindividual variance of serum ALP levels as well as rs2071699 in the FUT1 gene. Thus, there is evidence of interactions between ABO and FUT1/FUT2 on serum ALP levels, regardless of the possibility that rs2071699 in FUT1 is a proxy of rs1047781 in FUT2 in the Japanese population.

Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population.

The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.

The relationship between clinical pharmacokinetics of aripiprazole and CYP2D6 genetic polymorphism: effects of CYP enzyme inhibition by coadministration of paroxetine or fluvoxamine.

PURPOSE: To investigate the effects of coadministration of paroxetine or fluvoxamine on the pharmacokinetics of aripiprazole in healthy adult Japanese with different CYP2D6 genotypes. METHODS: Fourteen CYP2D6 extensive metabolizer (EM) and 14 CYP2D6 intermediate metabolizer (IM) subjects were coadministered a single oral dose of aripiprazole 3 mg after steady-state plasma concentrations of the SSRIs paroxetine (20 mg/day) or fluvoxamine (100 mg/day) were reached by repeated oral doses for 6-7 days. The pharmacokinetics of aripiprazole with and without coadministration of SSRIs were compared according to CYP2D6 genotypes. RESULTS: Coadministration of paroxetine, a potent CYP2D6 inhibitor, decreased systemic clearance (CL/F) of aripiprazole by 58 and 23% in CYP2D6 EMs and IMs, respectively, demonstrating that the percentage inhibition of CYP2D6 activity by coadministration of paroxetine was apparently greater in CYP2D6 EMs than in IMs. Coadministration of fluvoxamine, a less potent CYP3A4 inhibitor, decreased the CL/F of aripiprazole by 39% in CYP2D6 EMs and 40% in IMs, indicating the same inhibitory effect on CYP enzymes, regardless of the CYP2D6 genotype. Percent contribution of CYP2D6 to total CL/F (CYP2D6 plus CYP3A4) of aripiprazole estimated as a reduced percentage of CL/F by CYP enzyme inhibition was 62% for CYP2D6 EMs and 24% for IMs in paroxetine coadministration, and 40% for CYP2D6 EMs and 18% for IMs in fluvoxamine coadministration. CONCLUSIONS: There were marked differences in the degree of influence of paroxetine coadministration on the pharmacokinetics of aripiprazole between CYP2D6 EMs and IMs, but no apparent differences were found between two CYP2D6 genotypes in fluvoxamine coadministration. Aripiprazole can be used safely in combination with SSRIs that have a CYP enzyme-inhibitory action.

Inhibition of lipase activities by citrus pectin.

The oral administration of pectin to rats reduced and delayed the peak plasma triacylglycerol concentration. Pectin inhibited the hydrolysis of trioleoylglycerol emulsified with soybean phosphatidylcholine by pancreatic, carboxylester, and lingual lipases in a concentration-dependent manner. However, the effective concentration of pectin for lingual lipase was 100 times lower than that for pancreatic lipase. Pectin did not inhibit the tributyrin- and p-nitrophenylbutyrate-hydrolyzing activities by pancreatic and carboxylester lipase. When low molecular weight pectin was assayed, pectin at a molecular weight of 90,000 (MW 90) most strongly inhibited three lipase activities. When the effect of pH on pectin inhibition was analyzed using pancreatic lipase, strong inhibition was observed at an acidic pH (below pH 7.0). In the assay system, the pancreatic lipase protein levels in the supernatant and fat layer were estimated by Western blotting with an anti-pancreatic lipase antibody. Pectin reduced the amount of pancreatic lipase protein in the fat layer in a concentration-dependent manner and concomitantly increased that in the supernatant. These results suggest that pectin may interact with emulsified substrates and inhibit the adsorption of lipase to the surface of substrate emulsion.

Identification of CAG repeat-containing genes expressed in human brain as candidate genes for autosomal dominant spinocerebellar ataxias and other neurodegenerative diseases.

To obtain novel candidate genes for autosomal dominant spinocerebellar ataxia and other neurodegenerative disorders in which gene mutations remain unidentified, we screened a human fetal brain cDNA library using (CAG)(10) repeat probes. Sixteen cDNAs were isolated and mapped to chromosomes 1, 2, 3, 6, 9, 13, 15, 16, 22, and X. Although we failed to detect abnormal CAG repeat expansion within these genes in Japanese patients with inherited neurodegenerative diseases, these genes remain potential candidate genes for neurodegenerative diseases that feature anticipation.

Cloning and characterization of the human tektin-t gene.

Tektin-t is a part of the tektin protein family, the members of which form filamentous polymers in the walls of ciliary and flagellar microtubules. In mice, tektin-t protein has been localized to the tail of mature sperm, suggesting that it has a role in the formation of sperm flagella and/or sperm motility. In the present study, we have cloned a human orthologue of mouse haploid germ cell-specific tektin-t. The cloned human cDNA and the predicted amino acid sequence showed 82 and 83% identity with mouse tektin-t respectively. Included were a sequence conserved in the tektin B1 family, the TEKTIN2 motif, and the consensus sequence in the tektin protein family composed of nona-peptide. Northern blot analysis of mRNA isolated from various human organs showed that the transcript was approximately 1.7 kb in length and strongly expressed in the testis. Human (h-)tektin-t protein, having a molecular weight of 54 kDa, was exclusively expressed in the testis, whereas two additional stronger bands of 46 and 56 kDa existed in sperm. The h-tektin-t localized specifically to the principal piece of flagella and to the post-acrosomal region. The h-tektin-t gene was assigned to chromosome 1 by a radiation hybrid mapping technique.