Haplotype Structures of Common Variants of CYP2C8, CYP2C9, and ADRB1 Genes in a South Indian Population

Variability of CYP2C8 Polymorphisms in Three Jordanian Populations: Circassians, Chechens and Jordanian-Arabs

CYP2C8 is a member of Cytochrome P450 enzymes system. It plays an important role in metabolizing a wide range of exogenous and endogenous compounds. CYP2C8 is involved in the metabolism of more than 100 drugs, typical substrates include: anticancer agents, antidiabetic agents, antimalarial agents, lipid lowering drugs and many others that constitute 20% of clinically prescribed drugs. Genetic variations of CYP2C8 have been reported with different frequencies in different populations. These genetic polymorphisms can lead to differences in the efficacy and safety of different types of medications metabolized by CYP2C8. The aim of this study was to investigate the allele frequencies of CYP2C8*3 (rs10509681 and rs11572080) and CYP2C8*4 (rs1058930) polymorphisms in three populations living in Jordan; Circassians and Chechens and Jordanian-Arabs and compare those frequencies with other populations. A total of 200 healthy Jordanians, 93 Circassians and 88 Chechens were included in this study. Genotyping of CYP2C8*3 and CYP2C8*4 polymorphisms was done by using polymerase chain reaction (PCR) followed by Restriction Fragment Length Polymorphism (RFLP). Using the Chi-square test, we found that the prevalence of CYP2C8*3 and *4 among the three populations were significantly different. Moreover, the mutant allele CYP2C8*3 (416A) was only detected in the Jordanian-Arab population with an allele frequency of 0.082, while the mutant allele CYP2C8*4 (792G) was detected with frequencies of 0.065, 0.122, 0.017 in Jordanian-Arabs, Circassians and Chechens, respectively. As our results show, CYP2C8*3 was undetectable in our Circassians and Chechens samples, on the other hand, Circassians had the highest allele frequency of CYP2C8*4 compared to Chechens and Jordanian-Arabs. These genetic variations of the gene encoding the CYP2C8 drug metabolizing enzymes can lead to clinical differences in drug metabolism and ultimately variations in drug effectiveness and toxicities. This study provides evidence for the importance of personalized medicine in these populations and can be the foundation for future clinical studies.

How genetic variation was analyzed in phenytoin-induced gingival enlargement using single-nucleotide polymorphism of candidate gene CYP2C9?

Background:

Phenytoin-induced gingival overgrowth is an adverse drug reaction affecting few individuals, on phenytoin therapy for its antiepileptic effect. Analysis of genetic variation of CYP2C9*2 gene was done to identify the action of metabolic enzyme cytochrome P 450 on this drug. The main background of this publication is a quick review about one of the molecular techniques used to identify the single-nucleotide polymorphism (SNP) using polymerase chain reaction coupled with restriction fragment length polymorphism (PCR-RFLP).

Materials and Methods:

Deoxyribonucleic acid (DNA) was extracted from 5 ml of venous blood withdrawn from the individual, who had gingival overgrowth following phenytoin therapy. DNA was isolated, using the phenol-chloroform method. Isolated DNA was used for SNP analysis of CYP2C9*2 presentation. The basic procedure used for SNP analysis in our case was PCR-RFLP.

Results:

Genetic variation of CYP2C9*2 in our case was homomutant.

Conclusion:

The etiology of phenytoin-induced gingival overgrowth is always an enigma, but it is now becoming clearer that a multifactorial role may be involved in the cause. One of the factors analyzed was polymorphism of CYP2C9*2 gene and it was found to be homomutant in our case. Adverse drug reaction can be minimized, by either reducing the drug dosage or drug substitution. However, larger scale genome-wide study has to be carried out to confirm one of the etiopathogenesis as mutation of the CYP2C9 gene, in phenytoin-induced gingival overgrowth.

Distribution of CYP2C8 and CYP2C9 amino acid substitution alleles in South Indian diabetes patients: A genotypic and computational protein phenotype study

The CYP2C8 and CYP2C9 are two major isoforms of the cytochrome P450 enzyme family, which is involved in drug response, detoxification, and disease development. This study describes the differential distribution of amino acid substitution variants of CYP2C8 (*2-I269F & *3-R139K) and CYP2C9 (*2-C144R & *3-L359A) genes in 234 type 2 diabetes mellitus (T2DM) patients and 218 healthy controls from Andhra Pradesh, South India. Single locus genotype analysis has revealed that homozygous recessive genotypes of 2C8*2-TT (P ≤ .03), 2C9*2-TT (P ≤ .02), and heterozygous 2C9*3-AC (P ≤ .006) are seen to be increasingly present in the case group, indicating a significant level of their association with diabetes in Andhra population. The statistical significance of these recessive genotypes has persisted even under their corresponding allelic forms (P ≤ .01). Genotype association results were further examined by computational protein structure and stability analysis to assess the deleteriousness of the amino acid changes. The mutant CYP 2C8 and 2C9 (both *2 and *3) proteins showed structural drifts at both amino acid residue (range 0.43Å-0.77Å), and polypeptide chain levels (range 0.68Å-1.81Å) compared to their wild-type counterparts. Furthermore, the free energy value differences (range -0.915 to -1.38 Kcal/mol) between mutant and native protein structures suggests the deleterious and destabilizing potential of amino acid substitution polymorphisms of CYP genes. The present study confirms the variable distribution of CYP2C8 (*2 and *3) and CYP2C9 (*2 and *3) allelic polymorphisms among South Indian diabetic populations and further warrants the serious attention of CYP gene family, as a putative locus for disease risk assessment and therapy.

Inter and intra ethnic variation of vitamin K epoxide reductase complex and cytochrome P450 4F2 genetic polymorphisms and their prevalence in South Indian population

BACKGROUND:

Genetic variation in the vitamin K epoxide reductase complex (VKORC1) and cytochrome P450 4F2 (CYP4F2) genes were found to be strongly associated with the oral anticoagulant (OA) dose requirement. The distribution of genetic variation in these two genes was found to show large inter- and intra-ethnic difference.

MATERIALS AND METHODS:

A total of 470 unrelated, healthy volunteers of South Indians of either sex (age: 18-60 years) were enrolled for the study. A 5 ml of venous blood was collected and the genomic deoxyribonucleic acid (DNA) was extracted by using phenol-chloroform extraction method. Real-time quantitative polymerase chain reaction (RT-PCR) method was used for genotyping.

RESULTS:

The variant allele frequencies of VKORC1 rs2359612 (T), rs8050894 (C), rs9934438 (T) and rs9923231 (A) were found to be 11.0%, 11.8%, 11.7% and 12.0%, respectively. The variant allele VKORC1 rs7294 was (80.1%) more frequent and the variant allele CYP4F2 * 3 was found to be 41.8% in South Indians. The allele, genotype and haplotype frequencies of VKORC1 and CYP4F2 gene were distinct from other compared HapMap populations (P < 0.0001).

CONCLUSION:

The findings of our study provide the basic genetic information for further pharmacogenetic based investigation of OA therapy in the population.

Haplotype structures and functional polymorphic variants of the drug target enzyme aromatase (CYP19A1) in South Indian population

CYP19A1 gene product aromatase (CYP19A1) is a 58-kDa protein and belongs to the member of the cytochrome P450 superfamily, which facilitates the bioconversion of estrogens from androgens. Single-nucleotide polymorphisms (SNPs) of CYP19A1 affect the activity of the enzyme and have been implicated in the association of estrogen-dependent disease, prognosis, therapeutic efficacy, and toxicity of third-generation aromatase inhibitors (AIs). Based on ethnicity, the frequency distribution of CYP19A1 alleles will differ, and until now, no data are available for Indians. Using qRT-PCR with TaqMan assays, the frequencies of functionally important polymorphic variants of CYP19A1 gene were determined in 163 healthy subjects of South Indian origin. The observed frequencies of the CYP19A1 minor alleles for the SNPs rs4646 (T), rs10046 (T), rs700519 (T), rs700518 (G), rs727479 (G), rs4775936 (T), rs10459592 (G), rs749292 (A), rs6493497 (T), and rs7176005 (A) are 41.1 (35.8-46.4), 20.0 (15.6-24.3), 33.7 (28.6-38.9), 17.8 (13.6-21.9), 25.8 (21.0-30.5), 19.9 (15.6-24.3), 33.7 (28.6-38.9), 24.9 (20.2-29.5), 35.9 (30.7-41.1), and 35.9 (30.7-41.1), respectively. Strong linkage disequilibrium existed between CYP19A1 SNPs, and sixteen different haplotype structures with a frequency >1% were derived from all the 10 SNPs tested. The most common being the haplotype (H1) GCTATCTGTG with a frequency of about 17.8%. Gender-specific assessment showed significant difference in the allele frequency for rs749292 (p < 0.04), and greater inter-ethnic variation was detected in the distribution of CYP19A1 variants except for rs727479. Our results could provide preliminary insight for further pharmacogenetic investigations of AIs as well as for subsequent molecular epidemiological studies on the contribution of these variants to the occurrence and development of estrogen-dependent disease in South Indians.

Rapid identification of CYP2C8 polymorphisms by high resolution melting analysis

BACKGROUND

Cytochrome P450 (CYP) 2C8 is the principal enzyme responsible for the metabolism of arachidonic acid and various drugs, and influences drug-drug interactions and some associated diseases. Large interindividual differences in CYP2C8 enzymatic activity and several nonsynonymous genetic variations have been reported in different races. Therefore, how to identify CYP2C8 polymorphisms efficiently for genotyping in different populations is very important.

METHODS

A high resolution melting (HRM) analysis was used to characterize the CYP2C8 polymorphism. Genomic DNA was extracted from peripheral blood samples from 95 normal individuals in Taiwan. Nine exons of the CYP2C8 gene were screened by HRM analysis. All results were confirmed by direct DNA sequencing.

RESULTS

Five new single nucleotide polymorphisms (SNPs) were found in this study; two SNPs [1189G>A (D397N) and 1230C>T (G410G)] were in exon 8 and the others [1312G>C (E438Q), 1497T>C (A499A) and 1677delT (559delL)] were in exon 9. The 1497T>C (A499A) was the most common variant with an allele frequency of 20.53% but without amino acid substitution.

CONCLUSIONS

HRM analysis is a fast, reliable, accurate and cost-effective screening method for gene mutations, even very similar cDNA sequences with 83% identities, compared with CYP2C8 and CYP2C9.