Detection of mutations and polymorphism of N-acetyltransferase 1 gene in Indian, Malay and Chinese populations

Pharmacogenetics of common SNP affecting drug metabolizing enzymes: comparison of allele frequencies between European and Malaysian/Singaporean

Compared to Europe, data on genetic variation in genes transcribing drug metabolizing enzymes among Asian is limited due to ethnic diversity. Here we compare frequencies for clinically relevant single nucleotide polymorphism (SNP) commonly observed in drug metabolizing enzymes between European and Malaysian/Singaporean. Minor allele frequencies (MAF) for the indicated SNPs for European, South Asian and East Asian populations were obtained from the NCBI website (https://www.ncbi.nlm.nih.gov/snp). The SNP prevalence among Malaysian/Singaporean was characterized from gene association studies. Generally, some SNPs in CYP2D6 and CYP2C19 do not show good agreement between the two populations as to the MAF value obtained. CYP2D6*4 tends to be more common among European, whereas CYP2D6*10 is more common in Malays and Chinese among Singaporean. Regardless of different phenotype, MAF of CYP2D6*4 for Indians is similar to that seen by the European. Singaporeans show smaller MAF for CYP2C19*17 but higher CYP2C19*2 frequencies as opposed to European ones. Following growing attention to the contribution of CYP3A4/5, N-acetyltransferases (NAT2), thiopurine methyltransferase (TPMT) and uridine diphosphate glucuronosyltransferases (UGT)2B7 in predicting drug response across Europe, there are limited pharmacogenetics (PGx) studies examining the gene-drug interaction among Malaysian/Singaporean. To better understand the heterogeneity of the drug response, PGx studies for the abovementioned enzymes between ethnics in Malaysian/Singaporean should be identified.

Pharmacogenetics of common SNP affecting drug metabolizing enzymes: comparison of allele frequencies between European and Malaysian/Singaporean

Compared to Europe, data on genetic variation in genes transcribing drug metabolizing enzymes among Asian is limited due to ethnic diversity. Here we compare frequencies for clinically relevant single nucleotide polymorphism (SNP) commonly observed in drug metabolizing enzymes between European and Malaysian/Singaporean. Minor allele frequencies (MAF) for the indicated SNPs for European, South Asian and East Asian populations were obtained from the NCBI website (https://www.ncbi.nlm.nih.gov/snp). The SNP prevalence among Malaysian/Singaporean was characterized from gene association studies. Generally, some SNPs in CYP2D6 and CYP2C19 do not show good agreement between the two populations as to the MAF value obtained. CYP2D6*4 tends to be more common among European, whereas CYP2D6*10 is more common in Malays and Chinese among Singaporean. Regardless of different phenotype, MAF of CYP2D6*4 for Indians is similar to that seen by the European. Singaporeans show smaller MAF for CYP2C19*17 but higher CYP2C19*2 frequencies as opposed to European ones. Following growing attention to the contribution of CYP3A4/5, N-acetyltransferases (NAT2), thiopurine methyltransferase (TPMT) and uridine diphosphate glucuronosyltransferases (UGT)2B7 in predicting drug response across Europe, there are limited pharmacogenetics (PGx) studies examining the gene-drug interaction among Malaysian/Singaporean. To better understand the heterogeneity of the drug response, PGx studies for the abovementioned enzymes between ethnics in Malaysian/Singaporean should be identified.

Toxicogenetic profile and cancer risk in Lebanese

An increasing number of genetic polymorphisms in drug-metabolizing enzymes (DME) were identified among different ethnic groups. Some of these polymorphisms are associated with an increased cancer risk, while others remain equivocal. However, there is sufficient evidence that these associations become significant in populations overexposed to environmental carcinogens. Hence, genetic differences in expression activity of both Phase I and Phase II enzymes may affect cancer risk in exposed populations. In Lebanon, there has been a marked rise in reported cancer incidence since the 1990s. There are also indicators of exposure to unusually high levels of environmental pollutants and carcinogens in the country. This review considers this high cancer incidence by exploring a potential gene-environment model based on available DME polymorphism prevalence, and their impact on bladder, colorectal, prostate, breast, and lung cancer in the Lebanese population. The examined DME include glutathione S-transferases (GST), N-acetyltransferases (NAT), and cytochromes P-450 (CYP). Data suggest that these DME influence bladder cancer risk in the Lebanese population. Evidence indicates that identification of a gene-environment interaction model may help in defining future research priorities and preventive cancer control strategies in this country, particularly for breast and lung cancer.

A meta-analysis of the NAT1 and NAT2 polymorphisms and prostate cancer: a huge review

Studies revealing conflicting results on the role of NAT1 or NAT2 phenotypes on prostate cancer risk led us to perform a meta-analysis to investigate the association of these polymorphisms and prostate cancer risk. The meta-analysis included six studies with NAT1 genotyping (610 prostate cancer cases and 713 controls), and 10 studies with NAT2 genotyping (1,253 cases and 1,722 controls). The fixed effects odds ratio was 0.96 [95% confidence interval (95% CI): 0.75, 1.21; I(2) = 32.9%, P for heterogeneity = 0.189] for the NAT1 genotype, and the random effects odds ratio was 1.10 (95% CI: 0.87, 1.39; I(2) = 49.1%, P for heterogeneity = 0.039) for the NAT2 genotype. For NAT2 polymorphism, a statistically significant association between NAT2 polymorphism and prostate cancer appeared in Asians, but not in Caucasians. In conclusion, the NAT1 or NAT2 phenotypes detoxify carcinogens and their reactive intermediates are unlikely to be the cause of PCa development.

Genetic polymorphism in N-Acetyltransferase (NAT): Population distribution of NAT1 and NAT2 activity

N-Acetyltransferases (NAT) are key enzymes in the conjugation of certain drugs and other xenobiotics with an arylamine structure. Polymorphisms in NAT2 have long been recognized to modulate toxicity produced by the anti-tubercular drug isoniazid, with molecular epidemiologic studies suggesting a link between acetylator phenotype and increased risk for bladder cancer. Recent evidence indicates that the other major NAT isozyme, NAT1, is also polymorphic. The current analysis characterizes the main polymorphisms in both NAT2 and NAT1 in terms of their effect on enzyme activity and frequency in the population. Multiple NAT2 alleles (NAT2*5, *6, *7, and *14) have substantially decreased acetylation activity and are common in Caucasians and populations of African descent. In these groups, most individuals carry at least one copy of a slow acetylator allele, and less than 10% are homozygous for the wild type (fast acetylator) trait. Incorporation of these data into a Monte Carlo modeling framework led to a population distribution of NAT2 activity that was bimodal and associated with considerable variability in each population assessed. The ratio of the median to the first percentile of NAT2 activity ranged from 7 in Caucasians to 18 in the Chinese population. This variability indicates the need for more quantitative approaches (e.g., physiologically based pharmacokinetic [PBPK] modeling) to assess the full distribution of internal dose and adverse responses to aromatic amines and other NAT2 substrates. Polymorphisms in NAT1 are generally associated with relatively minor effects on acetylation function, with Monte Carlo analysis indicating less interindividual variability than seen in NAT2 analysis.

Phase I and II enzyme polymorphisms as risk factors for Barrett's esophagus and esophageal adenocarcinoma: a systematic review and meta-analysis

Although several studies have examined the association between phase I/II enzyme polymorphisms and esophageal adenocarcinoma (EAC) and/or Barrett's esophagus (BE), their overall findings remain unclear. We performed a systematic review and meta-analysis to determine whether phase I/II polymorphisms are independent risk factors for either BE or EAC. We employed keyword searches in multiple databases to identify studies published before October 1, 2007. Single-nucleotide polymorphisms (SNPs) examined in > or =3 studies were meta-analyzed to obtain a pooled estimate of effect. Meta-analysis suggested the minor allele for GSTP1 Val(105) conveys modest excess risk (odds ratio [OR](BE)= 1.50, 95% confidence interval [CI] 1.16-1.95; OR(EAC)= 1.20, 95% CI 0.94-1.54). No excess risk was observed with GSTM1 null (OR(BE)= 0.77, 95% CI: 0.56-1.08; OR(EAC)= 1.08, 95% CI: 0.79-1.48), GSTT1 null (OR(BE)= 1.35, 95% CI: 0.91-2.01; OR(EAC)= 0.84, 95% CI: 0.48-1.49), or CYP1A Val(462) (OR(EAC)= 0.89, 95% CI: 0.40-1.97). Insufficient data existed to meta-analyze remaining SNPs. Our review identified GSTP1(Ile105Val) as a possible risk factor for BE and EAC in Caucasian males. No excess risk was observed for other phase I/II polymorphisms with sufficient data to meta-analyze. Additional studies are needed to determine if GSTP1 conveys excess risk in females or non-Caucasians and to evaluate other phase I/II polymorphisms.

ArylamineN-Acetyltransferases: What We Learn from Genes and Genomes

Arylamine N-acetyltransferases (NATs) are phase II xenobiotic metabolizing enzymes, catalyzing acetyl-CoA-dependent N- and O-acetylation reactions. All NATs have a conserved cysteine protease-like Cys-His-Asp catalytic triad inside their active site cleft. Other residues determine substrate specificity, while the C-terminus may control hydrolysis of acetyl-CoA during acetyltransfer. Prokaryotic NAT-like coding sequences are found in >30 bacterial genomes, including representatives of Actinobacteria, Firmicutes and Proteobacteria. Of special interest are the nat genes of TB-causing Mycobacteria, since their protein products inactivate the anti-tubercular drug isoniazid. Targeted inactivation of mycobacterial nat leads to impaired mycolic acid synthesis, cell wall damage and growth retardation. In eukaryotes, genes for NAT are found in the genomes of certain fungi and all examined vertebrates, with the exception of canids. Humans have two NAT isoenzymes, encoded by highly polymorphic genes on chromosome 8p22. Syntenic regions in rodent genomes harbour two Nat loci, which are functionally equivalent to the human NAT genes, as well as an adjacent third locus with no known function. Vertebrate genes for NAT invariably have a complex structure, with one or more non-coding exons located upstream of a single, intronless coding region. Ubiquitously expressed transcripts of human NAT1 and its orthologue, murine Nat2, are initiated from promoters with conserved Sp1 elements. However, in humans, additional tissue-specific NAT transcripts may be expressed from alternative promoters and subjected to differential splicing. Laboratory animals have been widely used as models to study the effects of NAT polymorphism. Recently generated knockout mice have normal phenotypes, suggesting no crucial endogenous role for NAT. However, these strains will be useful for understanding the involvement of NAT in carcinogenesis, an area extensively investigated by epidemiologists, often with ambiguous results.

N-Acetyltransferase-1 gene polymorphisms and correlation between genotype and its activity in a central Chinese Han population

BACKGROUND

We investigated the arylamine N-acetyltransferase-1 (NAT1) gene polymorphisms and the correlation between genotype and phenotype in a Chinese Han population.

METHODS

Peripheral blood from 140Han people were collected and analyzed for NAT1 genotypes by allele-specific PCR combining with PCR-based restriction fragment length polymorphism-based procedure. The NAT1 phenotype were determined according to the NAT1 enzyme kinetics in leukocytes by HPLC method and the values of intrinsic clearance (Cl(int)) and V(max) and Michaelis constant (K(m)) of NAT1 were calculated.

RESULTS

The NAT1 genotype of Chinese Han populations was distinguished accurately and the NAT1 activity were detected in 32 objects with different genotypes. The allelic frequencies of NAT1*3, NAT1*4, NAT1*10 and NAT1*11 from 140 Han people, were 0.082, 0.496, 0.40 and 0.022, respectively. Compared with the activity of wild genotype NAT1 *4/*4, the activity of the homozygote or heterozygote NAT1*10 genotype which includes the NAT1 *4/*10, the NAT1 *10/*10 and the NAT1 *3/*10 was significantly high (p<0.05). The activity of the NAT1 *11/*11 and NAT1 *4/*11 was lower than that of the homozygote or heterozygote NAT1*10 genotype (p<0.05), but no difference with the activity of wild genotype and the NAT1 *4/*3 and NAT1 *3/*3.

CONCLUSION

The distribution of the NAT1 genotype in a Chinese Han population was different from that in other countries. The activity of NAT1 showed significant variance from leukocytes with different genotypes.

Are polymorphisms of N-acetyltransferase genes susceptible to primary liver cancer in Luoyang, China?

AIM: To identify whether the polymorphisms of the N-acetyltransferase (NAT) genes are susceptible to primary liver cancer (PLC) in Luoyang, a PLC low-incidence area of China.

METHODS: The NAT1 and NAT2 genotypes of 96 PLC cases and 173 controls were determined by PCR-RFLP. Both interaction between NAT1 or NAT2 and environmental risk factors were analyzed based on case control study.

RESULTS: Compared to the control group, the frequencies of alleles NAT1*3, NAT1*4, NAT1*10, NAT1*14B and alleles NAT2*4, NAT2*6, NAT2*7 in PLC group showed no statistically significant difference (χ² = 2.61 and 4.16, respectively, both P>0.05). The frequencies of NAT1 genotypes NAT1*3/*3, NAT1*3/*4, NAT1*3/*10, NAT1*3/*14B, NAT1*4/*4, NAT1*4/*10, NAT1*4/*14B, NAT1*10/*10, NAT1*10/*14B, and NAT2 genotypes NAT2*4/*4, NAT2*4/*6, NAT2*4/*7, NAT2*6/*6, NAT2*6/*7 and NAT2*7/*7 also had no statistically significant difference between the two groups (χ² = 11.86 and 2.94 respectively both, P>0.05). Neither the frequencies of rapid and slow NAT1 acetylators nor the frequencies of rapid and slow NAT2 acetylators were significantly different between the two groups (χ² = 0.598 and 0.44, respectively, both P>0.05). The interaction between NAT1*10 and occupational exposures was found significant with an odds ratio of 3.40 (χ² = 8.42, P = 0.004, OR 95%CI:1.03-11.22). But no interaction was found between NAT2 and any environmental risk factors.

CONCLUSION: The polymorphisms of NAT1 and NAT2 are not susceptible to PLC in Luoyang. Allele NAT1*10 interacts with occupational exposures.

Pharmacokinetics of a novel N-methyl-D-aspartate receptor antagonist (SM-18400): identification of an N-acetylated metabolite and pre-clinical assessment of N-acetylation polymorphism

(S)-9-chloro-5-[p-aminomethyl-o-(carboxymethoxy)phenylcarbamoylmethyl]-6,7-dihydro-1 H,5 H-pyrido[1,2,3-de]quinoxaline-2,3-dione hydrochloride trihydrate (SM-18400) was given intravenously to rats and dogs and its pharmacokinetics was investigated. By LC/MS/MS analysis, the major metabolite in the rat serum was identified as N-acetylated SM-18400 (SM-NAc). In rats, AUC ratio of SM-NAc to SM-18400 was approximately 50%. However, 71% of the dose was excreted as unchanged SM-18400 and only 9.8% as SM-NAc in the urine and bile, indicating that the contribution of N-acetylation clearance (CL(NAc)) to the total clearance (CL(tot)) is limited to 10-30% in rats. No SM-NAc or other metabolites were detected in the dog serum, urine or bile. The in vitro intrinsic clearance (CL(int), ml/min/mg cytosolic protein) of N-acetyltransferase (NAT) activities of dog liver cytosol towards SM-18400 and hepatic N-acetylation clearance (CL(NAc), ml/min/kg body weight) estimated by well-stirred model were both only 5% of the respective rat value, well reflecting the relative in vivo CL(NAc)/CL(tot) ratios. CL(int) values for human liver cytosol samples (n = 4) and estimated CL(NAc) were all less than 18% and 7% of the rat, respectively. Based on these results, we concluded that the CL(NAc)/CL(tot) of human would be small enough to avoid major inter-individual variance in SM-18400 pharmacokinetics due to N-acetylation polymorphism. In addition, even a human liver cytosol sample lacking polymorphic NAT2 activity as determined by sulfamethazine (SMZ) N-acetylation analysis, proved capable of acetylating SM-18400, suggesting that NAT2 is not the major enzyme responsible for N-acetylation of SM-18400 in human. This fact would also reduce the risk of N-acetylation polymorphism playing a role in clinical use of this drug.

Polymorphism of N-acetyltransferase 1 and correlation between genotype and phenotype in a Thai population

OBJECTIVES

To analyze the common allele frequencies of the arylamine-N-acetyltransferase 1 (NAT1) and examine the relationship between genotype and phenotype in a Thai population.

METHODS

Peripheral blood samples from 233 Thai individuals were analyzed for genotype using polymerase chain reaction with restriction fragment-length polymorphism assays and for phenotype by determination of NAT1 enzyme kinetics in leukocytes using para-aminobenozic acid as a specific substrate.

RESULTS

Of 466 NAT1 alleles assayed, the frequency of the NAT1*4 allele (wild-type) was 0.504 (95%CI 0.458-0.551) and those of the NAT1*10, *3 and *11 alleles were 0.438 (0.392-0.484), 0.034 (0.02-0.055) and 0.024 (0.012-0.042), respectively. Neither NAT1*14A nor *14B alleles were found in this studied population. The activity of NAT1 enzyme from peripheral blood leukocytes determined in 47 subjects was found to vary widely. The intrinsic clearance and Vmax values of NAT1 enzymes with genotypes NAT1 *4/*4, *10/*10 and *4/ *10 were not significantly different.

CONCLUSION

The frequency distribution of the major NAT1 alleles in the Thai population has a similar pattern to some Asian populations; however, racial differences among Asian populations need further clarification.

Relationship between NAT1 genotype and phenotype in a Japanese population

NAT1, which biotransforms many carcinogens, is genetically polymorphic. This polymorphism has been postulated as a mechanism for susceptibility differences in cancer, possibly due to NAT1 activity differences. However, the relationship between NAT1 genotype and phenotype is not clear. In our study of 110 Japanese, the frequency of the NAT1*10 allele (0.53, 95% confidence interval 0.46-0.59) was higher than others have observed in Caucasians (0.16). From genotype frequency studies, 26.4% of the subjects belonged to the NAT1*10/*10 genotype, 53.6% to the NAT1*4/*10 genotype and 20% to the NAT1*4/*4 genotype. Neither NAT1*3 nor NAT1*11 genotype was seen in these subjects. In female subjects, we found higher NAT1 activity in NAT1*4/*10 subjects than in NAT1*4/*4 subjects (n = 49; 2.63 versus 2.16 nmol/min/mg protein). NAT1 activity-difference between NAT1*4/*10 and NAT1*10/*10 was not statistically significant. Thus, not only the presence of NAT1*10 allele, but also other factors are suspected of increasing NAT1 activities. After full sequencing of 10 subjects, five individuals having the highest activities and five individuals having the lowest activities, we found NAT1*18A and NAT1*18B to be in the high activity group and the low activity group, respectively. The genotypes containing these variants were heterozygous, i.e. NAT1*4/*18A and NAT1*4/*18B. Due to rare frequencies of these variants, they cannot be considered as other effective, genetic factors on NAT1 activity. Age and tobacco smoking did not affect the relationship between NAT1 genotype and phenotype.

Arylamine N-acetyltransferase 1 (NAT1) genotypes in a Lebanese population

The frequency distributions of human N-acetyltransferase 1 (NAT1*) alleles in various ethnic groups are largely unknown. This lack of information is in contrast to the many studies of ethnic differences in NAT2* alleles and phenotypes. Increasing interest in NAT1 due to its potential roles in carcinogen metabolism and cancer risk makes it desirable to know the distribution of NAT1* alleles in various populations. Using a polymerase chain reaction-restriction fragment length polymorphism genotyping assay, the frequency of NAT1* alleles in a Lebanese population was determined. Of 84 NAT1* alleles assayed, 56% were NAT1*4. Alleles NAT1*3, *10, and *14 were found at frequencies of 0.036, 0.107, and 0.238, respectively. Five additional alleles (6%) differed from previously reported alleles. Nearly 50% of the population were heterozygous for a NAT1*14 allele. The unusually high frequency of NAT1*14 alleles in Lebanese may be useful for epidemiological studies of the effects of the NAT1 polymorphism in this population.

Rapid detection of CYP1A1, CYP2D6, and NAT variants by multiplex polymerase chain reaction and allele-specific oligonucleotide assay

Drugs and carcinogens are excreted from the body after metabolic conversion involving enzymes mediating oxidative metabolism and conjugation. Many of the corresponding genes exhibit functional polymorphisms that contribute to individual cancer susceptibility. To increase the efficiency and to facilitate genotyping, we developed a combined approach (PCR-ASO) which includes multiplex PCR and allele-specific oligonucleotide (ASO) hybridization. PCR primer pairs were used to amplify the following alleles/variants: CYP1A1*1, *2A, *2B; CYP2D6*3, *4; NAT1*4, *3, *10, *11, *14, *15; and NAT2*4, *5A, *5B, *5C, *6A, *7B. The products were dot-blotted and polymorphisms were detected by hybridization with ASO probes for both wild-type and variant sites in parallel. This approach was validated by genotyping DNA samples from a French-Canadian population that was previously analyzed by PCR-RFLP. The variants frequencies were compared with the data on other populations available in the literature. The PCR-ASO assay appears to be simple, efficient, and cost-effective, particularly if a large number of samples are to be screened for several DNA variants. This approach has potential for automation with microplates and robotic workstations for high throughput.