Pharmacogenetics of the major polymorphic metabolizing enzymes

There is increasing information available on the existence of polymorphisms in genes encoding xenobiotic metabolizing enzymes and the functional significance of many of these. In addition to genes long recognized as being polymorphic, such as CYP2D6, CYP2C19 and CYP2C9, there is now information available on the existence of polymorphisms in other cytochrome P450 genes such as CYP2A6, CYP2B6 and CYP2C8. With respect to phase II metabolism, polymorphisms in GSTM1, GSTT1, NAT2 and TPMT are well understood but information is also emerging on other GST polymorphisms and on polymorphisms in the UDP-glucuronosyltransferases and sulfotransferases. The availability of comprehensive information on the occurrence and functional significance of polymorphisms affecting drug metabolism should facilitate their application to pharmacogenomic profiling.     

Correlation of xenobiotic-metabolizing enzymes,oxidative stress and NFκB signaling with histological grade and menopausal status in patients with adenocarcinoma of the breast

BackgroundAdenocarcinoma of the breast is the most common cancer worldwide and accounts for the highest morbidity and mortality. The increasing global incidence of breast cancer emphasizes the need to understand the molecular mechanisms of breast tumorigenesis. The present study was designed to correlate changes in xenobiotic-metabolizing enzymes (XME), oxidative stress and NFκB signaling with histological grading and menopausal status in breast cancer patients.MethodSixty breast cancer patients histologically categorized as grades I, II and III, and as pre- and postmenopausal were chosen for the study. We analyzed phase I and phase II XME activities as well as the expression of the CYP isoforms CYP1A1 and CYP1B1, oxidative stress markers, and the expression of NFκB family members in tumor and adjacent tissues by immunohistochemical localization and Western blot analyses.ResultsThe breast tumors analyzed in the present study were characterized by increased activities of xenobiotic-metabolizing enzymes and enhanced oxidative damage to lipids, proteins, and DNA associated with variations in the expression of NFκB family members. The magnitude of the changes was however more pronounced in premenopausal patients and in grade III breast tumors.ConclusionThe present study delineates the correlation between XME-mediated oxidative stress and NFκB signaling that leads to the development of breast cancer.     

Update: genetic polymorphism of drug metabolizing enzymes in humans

The cytochrome P450 (P450 or CYP) monooxygenases, CYP2D6, CYP2C19, CYP2E1 and CYP2C9, and non-P450 monooxygenases, N-acetyltransferase, thioprine methyltransferases and dihydropyrimidine dehydrogenase, all display polymorphism. CYP2D6 and CYP2C19 have been studied extensively and, despite their low abundance in the liver, they have been found to catalyse the metabolism of many drugs. CYP2D6 has many allelic variants, whereas CYP2C19 has only two. Most variants are translated into inactive, truncated proteins or fail to express protein. There is, as yet, no clear information about CYP2E1 polymorphism. In addition, genetic differences in certain foreign-compound metabolizing enzymes, such as Phase II enzymes, have been shown to be associated with an increased risk of developing environmentally and occupationally related diseases such as cancer. When two drugs that are substrates of a polymorphic CYP enzyme are administered concomitantly during drug therapy, each will compete for that enzyme and competitively inhibit the metabolism of the other substrate. This can result in toxicity. Patients who are poor metabolizers (PMs), extensive metabolizers (EMs) and ultrarapid metabolizers (URMs) can be identified. Having such information will help in determining the appropriate dosage of certain drugs when treating patients with an inherited abnormality of a drug-metabolizing enzyme. In view of the remarkable progress in this particular field, it is to be expected that more genetic polymorphisms will be discovered in the near future.     

Three novel polymorphic sequence variants in the type I collagen gene COL1A1, the main disease locus for Osteogenesis Imperfecta

Three novel polymorphic variants were found within COL1A1 genomic sequence (accession number AF017178) while screening several patients in the search of OI causal mutations. The three polymorphisms, located in intron 12, exon 26, and intron 29, respectively, can be detected by PCR amplification and digestion with appropriate restriction enzymes (Mbo II, Bst NI, Pvu II, respectively). Allelic frequencies within the Italian population were calculated.     

Naringenin modulates circulatory lipid peroxidation, anti-oxidant status and hepatic alcohol metabolizing enzymes in rats with ethanol induced liver injury

We have investigated the modulatory efficacy of naringenin on circulatory lipid peroxidation and anti-oxidant status, hepatic alcohol metabolizing enzymes in rats with ethanol induced hepatotoxicity. Rats were divided into four groups: groups 1 and 2 received isocaloric glucose and 0.5% carboxymethyl cellulose; groups 3 and 4 received 20% ethanol equivalent to 6 g/kg body weight everyday for the total experimental period of 60 days. In addition, groups 2 and 4 were given naringenin (50 mg/kg) everyday for the last 30 days of the experiment. The results showed significantly elevated levels/activities of bilirubin, alkaline phosphatase (ALP), lactate dehydrogenase (LDH), thiobarbituric acid reactive substances (TBARS), lipid hydroperoxides (LOOH), conjugated dienes (CD) and phase I enzymes, and significantly lowered the activities of alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), superoxide dismutase (SOD), catalase (CAT) and phase II enzymes in ethanol-fed rats as compared to those of the control. Supplementation with naringenin for the last 30 days of the experiment to ethanol-fed rats, significantly decreased the levels/activities of bilirubin, ALP, LDH, TBARS, LOOH, CD and phase I enzymes, and significantly elevated the activities of ADH, ALDH, SOD, CAT and phase II enzymes as compared to control rats. These findings suggest that naringenin can effectively modulate the hepatic alcohol metabolizing enzymes in rats with ethanol induced liver injury.     

The epidemiology of childhood leukemia with a focus on birth weight and diet

Leukemia is the most common childhood cancer and a major source of morbidity and mortality. The etiology of childhood leukemia remains largely unknown. Cytogenetic abnormalities determine disease subtypes, prognosis, clinical presentation, and course and may help in discovering etiological factors. Epidemiologic investigations of leukemia are complicated by many factors, including the rarity of the disease, necessitating careful study design. Two emerging areas of interest in leukemia etiology are birth weight and diet. High birth weight has been associated with increased risk of childhood leukemia. The biological mechanism behind this association may involve insulin-like growth factor I (IGF-I), which is associated with high birth weight. IGF-I may act by increasing the absolute number of stem cells available for transformation, stimulating the growth of cells that are already transformed, or a combination of effects. Diet has been linked with leukemia. Maternal dietary DNA topoisomerase II (DNAt2) inhibitor intake is associated with infant acute myeloid leukemia (AML) with the MLL gene translocation. Increased intake of fruits and vegetables has been associated with decreased leukemia risk and, relatedly, lack of maternal folate supplementation has been associated with increased childhood leukemia risk, possibly by causing DNA hypomethylation and increased DNA strand breaks. Methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms modify this risk.     

HLA class I-, complement C4- and 21-hydroxylase probes in the genetic analysis of 21-hydroxylase deficiency

In order to develop an optimal strategy for the prenatal diagnosis of steroid 21-hydroxylase (EC 1.14.99.10) deficiency, we investigated 16 affected families with salt wasting syndrome. Genomic DNA derived from peripheral white blood cells was digested with 6 different restriction enzymes. Hybridisation was carried out with DNA-probes of the HLA class I region, the 21-hydroxylase- and the complement C4 genes. All the families were informative in at least three different loci. Twelve out of the 16 families were informative by neutral polymorphisms or disease related variants of the 21-hydroxylase gene or the adjoining C4 locus. The reliability of prediction in these cases exceeded 99%. The remaining 4 families were informative only in the HLA class I region, tantamount to a reliability of prediction of about 98%. In none of the cases did we have to fall back on semiquantitative gene dose assessments. We further describe new polymorphisms in the 21-hydroxylase region for the enzyme Pvu II and EcoR V.     

Drug metabolism in carcinogenesis and cancer chemotherapy.

Cytotoxic drugs have become invaluable for the clinical oncologist in the treatment of neoplastic disease. Frequently, these therapeutic agents are used in combination in order to combat the heterogeneity imposed by the variable tumor cell biochemistry of the neoplastic cell population. Hence, one could argue polypharmacy has become the rule rather than the exception in cancer chemotherapy. The use of such regimens obviously increases the potential for drug-drug interactions and also may potentiate the effects of interindividual variation in drug metabolism. Altered expression of drug metabolizing enzymes may also predispose certain individuals to cancer through enhanced metabolic activation and decreased detoxication of environmental, dietary and possibly endogenous procarcinogens. Many anticancer drugs can be considered as prodrugs which require metabolic activation to exert their selective cytotoxic effects. Recent molecular and biochemical advances have increased our understanding of the factors which govern the regulation of drug metabolizing enzymes and have improved our knowledge of the metabolism and action of anticancer agents. The aim of this review is not to exhaustively document all the work in the area of drug metabolism in relation to cancer, but to provide a comprehensive update of some of the recent advances in drug metabolism which have helped to rationalize the mechanism of action of some anticancer drugs and which may help to optimize future patient selection for certain novel chemotherapeutic regimens. This review also discusses some of the more recent breakthroughs in the area of carcinogenesis and highlights directions for future studies.     

Polymorphisms in UDP glucuronosyltransferase genes: functional consequences and clinical relevance.

As glucuronidation is a major process for the metabolism and removal of lipophilic chemicals, polymorphic variations in genes encoding the enzymes involved in this process, the UDP glucuronosyltransferases (UGT), may have a significant impact on our capacity to detoxify and eliminate drugs and toxins. Although 24 human UGT genes have been identified to date, only polymorphisms in five UGTs, viz. UGT1A1, UGT1A6, UGT2B4, UGT2B7 and UGT2B15 have been described. Polymorphisms in UGT1A1, the major bilirubin-glucuronidating form, often result in a decreased capacity to glucuronidate bilirubin, such as observed in Gilbert Syndrome and some forms of perinatal jaundice. The frequencies of individual UGT1A1 polymorphisms show extensive variability across ethnic groups. Two variants of UGT1A6 and UGT2B4 and one variant of UGT2B7 and UGT2B15 have been identified. However, the clinical significance of these variants is unclear. More UGT polymorphisms will undoubtedly be discovered when the human genome is sequenced. However, unless the UGT in question is responsible for the exclusive metabolism of a particular drug or chemical (e.g. UGT1A1 and bilirubin) or is the predominant or only UGT present in the cell, it is unlikely that these polymorphisms will be of major clinical significance.     

Phase I Metabolic Genes and Risk of Lung Cancer: Multiple Polymorphisms and mRNA Expression

Polymorphisms in genes coding for enzymes that activate tobacco lung carcinogens may generate inter-individual differences in lung cancer risk. Previous studies had limited sample sizes, poor exposure characterization, and a few single nucleotide polymorphisms (SNPs) tested in candidate genes. We analyzed 25 SNPs (some previously untested) in 2101 primary lung cancer cases and 2120 population controls from the Environment And Genetics in Lung cancer Etiology (EAGLE) study from six phase I metabolic genes, including cytochrome P450s, microsomal epoxide hydrolase, and myeloperoxidase. We evaluated the main genotype effects and genotype-smoking interactions in lung cancer risk overall and in the major histology subtypes. We tested the combined effect of multiple SNPs on lung cancer risk and on gene expression. Findings were prioritized based on significance thresholds and consistency across different analyses, and accounted for multiple testing and prior knowledge. Two haplotypes in EPHX1 were significantly associated with lung cancer risk in the overall population. In addition, CYP1B1 and CYP2A6 polymorphisms were inversely associated with adenocarcinoma and squamous cell carcinoma risk, respectively. Moreover, the association between CYP1A1 rs2606345 genotype and lung cancer was significantly modified by intensity of cigarette smoking, suggesting an underling dose-response mechanism. Finally, increasing number of variants at CYP1A1/A2 genes revealed significant protection in never smokers and risk in ever smokers. Results were supported by differential gene expression in non-tumor lung tissue samples with down-regulation of CYP1A1 in never smokers and up-regulation in smokers from CYP1A1/A2 SNPs. The significant haplotype associations emphasize that the effect of multiple SNPs may be important despite null single SNP-associations, and warrants consideration in genome-wide association studies (GWAS). Our findings emphasize the necessity of post-GWAS fine mapping and SNP functional assessment to further elucidate cancer risk associations.     

Pharmacogenomics of drugs affecting the cardiovascular system.

The variability in drug response originates partly from genetics, with possible consequences for drug efficacy, adverse effects, and toxicity. Until now, pharmacogenetics mainly indicated the best known source of variability, that is, the variability caused by drug metabolism. However, simultaneous progress in the knowledge of biochemical targets of drugs and of the human genome, together with the development of new technologies, revealed many new sources of human genetic variation, e.g., in receptors or transporters. Drugs are metabolized by various polymorphic phase I enzymes, including cytochromes P450 (CYP). Among them, the most relevant for the metabolism of cardiovascular drugs are CYP3A4, CYP2C9 or CYP2C19, and CYP2D6. The role of phase II enzymes is limited with regard to cardiovascular drugs biotransformation, but some polymorphisms (glutathion-S-transferase; GSH-T) are linked to cardiovascular risk. Phase III proteins or transporters, especially from the ABC family, must also be considered, as their polymorphisms affect cholesterol and other sterols transport. Among pharmacological targets, some proteins were identified as involved in interindividual variations in the response to cardiovascular drugs. Some examples are apolipoprotein E, angiotensin-converting enzyme, and the beta-adrenergic receptor. From the risk concept emphasizing impaired metabolism and adverse effects, we now moved to an approach, which is a personalized, genotype-dependent adaptation of therapy.     

Cardiovascular pharmacogenomics: current status,future prospects

Pharmacogenomics is a field dedicated to exploring the contribution of genetics to interindividual variability in drug response. A goal of cardiovascular pharmacogenomics is to guide cardiovascular drug development and selection so as to optimize therapeutic benefit and minimize the potential for toxicity. Genetic-based differences in drug metabolism have long been recognized but just now are on the verge of wider clinical application. Differences in efficacy of cardiovascular drugs (independent of drug concentration) based on common genetic variations (polymorphisms) only recently have begun to be explored, but the potential for clinical application appears promising. Examples are presented of important pharmacodynamic effects of genetic variants on several drugs, including those in antiarrhythmic, reninangiotensin, beta-blocker, lipid-lowering, and antithrombotic classes. Principles of pharmacogenomics applied to drug metabolism are discussed that are relevant to drug development and clinical use, and examples are given for CYP450 phase I enzymes, phase II enzymes, and drug transporters. Challenges in establishing true pharmacogenetic associations are discussed, and current and future clinical potential is summarized. Rapid research progress and initial clinical applications with pharmacogenomics are foreseen in the near future.     

Haplotype analysis and identification of genes for a complex trait: examples from schizophrenia

For more than a decade there has been intensive research into the genetic etiology of schizophrenia, yet it is only recently that the first findings of promising genes associating with the disorder have been reported. Linkage analyses in families collected from different populations have provided relatively well defined genomic loci. These have been typically followed by fine mapping studies using single nucleotide polymorphisms (SNPs). A number of analysis programs have been produced to test SNPs and their haplotypes for association. Typically association has been established to specific haplotypes representing an allelic variant of the corresponding gene. The inherent problem of multiple testing in the analysis of haplotypes needs to be addressed fully, to determine if any of these recent findings can be considered as confirmed susceptibility genes for schizophrenia. However, informative haplotypes have provided a way to define allelic variants of genes associated with schizophrenia in numerous study samples, and are a useful tool in characterizing the extent of allelic diversity of putative schizophrenia susceptibility genes within different populations.     

Correlation between circulating levels of von Willebrand's antigen II and von Willebrand factor: discrimination between type I and type II von Willebrand's disease

Classification of the subtypes of von Willebrand's disease (vWd) has been based on a quantitative deficiency or an abnormal multimeric composition of von Willebrand factor (vWf). Although the co-deficiency of a second protein, von Willebrand's antigen II (vW AgII), had been previously recognized, its concentration in a relatively large number of normal individuals or patients with well-defined vWd variants had not been studied. The plasma from patients with type I, IIA, IIB, IIC, and III (severe) vWd was evaluated, and the concentrations of vW AgII and vWf were determined. Although patients with type I and III vWd had reduced levels of both proteins, the plasma vW AgII concentration was normal in patients with type II vWd. Analysis of the results indicates that type I and type II variants can be discriminated with greater than 80% accuracy by comparison of results of these two antigenic assays. The normal levels of vW AgII in type II variants suggest a possible difference in the pathophysiology of type I and type II vWd.     

Genetic polymorphisms of cytochrome P450 among patients with Balkan endemic nephropathy (BEN)

OBJECTIVES: The concept of multifactorial etiology of BEN anticipates that a combination of polymorphic gene variants and various environmental factors causes an increased risk for the disease. CYP enzymes play a key role in the metabolic activation of environmental chemicals and toxins. CYP3A enzymes are particularly relevant for xenobiotic metabolism because of their broad substrate specificity and abundant expression in the human liver, intestine, and kidney. Previous phenotyping analysis on CYP2D6 enzyme activity in BEN patients proposed a modifying effect of CYP2D6 gene variants on BEN risk, but it was not approved with molecular-genetic methods. The aim of the current case-control study was to compare the frequency of CYP2D6 and CYP3A5 polymorphisms, as well as one CYP3A4 promoter variant in BEN patients and controls in order to investigate a possible association between individual genetic variations in these genes and susceptibility to BEN. DESIGN AND METHODS: Ninety-six nonrelated Bulgarian BEN patients from endemic villages in the Vratza district and 112 healthy Bulgarians from nonendemic areas (controls) were genotyped. Identification of alleles was done by allele-specific PCR or by rapid-cycle amplification on the LightCycler, followed by sequence-specific detection. RESULTS: The UM, PM, and EM + IM genotype frequencies of CYP2D6 did not differ significantly between the two groups (P > 0.05). The CYP3A4*1B allele was only found in the heterozygous form, with allelic frequencies of 5.21% in the patients and 2.23% in the healthy individuals (P = 0.11). The CYP3A5*1 allele was more prevalent in BEN patients with a frequency of 9.38% compared to 5.36% in the controls and was associated with a higher risk for BEN (OR 2.41, 95% CI 1.09-5.33) (P = 0.02). CONCLUSIONS: Our results demonstrate that the CYP3A5*1 allele, previously reported as a marker for CYP3A5 expression in human kidney, is associated with increased risk for BEN, while CYP3A4*1B and CYP2D6 genotypes do not significantly modify the risk for the disease.     

Allele frequencies for glutathione S-transferase and N-acetyltransferase 2 differ in African population groups and may be associated with oesophageal cancer or tuberculosis incidence.

Glutathione S-transferase (GST) and arylamine N-acetyltransferase 2 (NAT2) metabolise many environmental and chemotherapeutic agents, which influence susceptibility to disease. Polymorphisms in these enzymes result in different host phenotypes and contribute to different disease profiles or responses to toxic or chemotherapeutic agents, depending on their frequency in different populations. GST and NAT2 polymorphisms were investigated in different population groups, including African populations, and a range of allelic frequencies have been observed. The GSTM1 null genotype frequency, reported in this paper in two South African ethnic groups, is the lowest reported (0.19-0.21). In contrast, these same groups have a high GSTT1 null frequency (0.41-0.54), which is considerably higher than in African-Americans, or other Africans. The GSTT1 null frequency is comparable to the Chinese, a population with a very high oesophageal cancer incidence, similar to that in the African group. The frequency of the GSTPi Val105 variant in the South African Xhosas was also high (0.53), differing significantly from the low frequency in other Africans. These variants could therefore be associated with high cancer susceptibility. In addition, the high proportion of NAT2 "fast" alleles may partially explain the high tuberculosis prevalence in South Africans, due to reduced isoniazid efficacy in the presence of rapid acetylation.     

Database analysis and gene discovery in pharmacogenetics.

The global genome research effort has resulted in the creation of extensive DNA and protein sequence databases that are a valuable resource for the identification of new genes and polymorphic variants of enzymes of pharmacogenetic interest. Previously undescribed members of gene families with novel functions and substrate specificities can be identified by database searching and sequence alignment strategies. Since the expressed sequence tag (EST) database contains sequences from many individuals, it can be searched for evidence of polymorphisms that can significantly influence enzyme function. The different approaches to these forms of analysis are reviewed and illustrated with examples from the glutathione transferase gene family.     

Haplotype analysis and identification of genes for a complex trait: examples from schizophrenia

For more than a decade there has been intensive research into the genetic etiology of schizophrenia, yet it is only recently that the first findings of promising genes associating with the disorder have been reported. Linkage analyses in families collected from different populations have provided relatively well defined genomic loci. These have been typically followed by fine mapping studies using single nucleotide polymorphisms (SNPs). A number of analysis programs have been produced to test SNPs and their haplotypes for association. Typically association has been established to specific haplotypes representing an allelic variant of the corresponding gene. The inherent problem of multiple testing in the analysis of haplotypes needs to be addressed fully, to determine if any of these recent findings can be considered as confirmed susceptibility genes for schizophrenia. However, informative haplotypes have provided a way to define allelic variants of genes associated with schizophrenia in numerous study samples, and are a useful tool in characterizing the extent of allelic diversity of putative schizophrenia susceptibility genes within different populations.     

The p53 inhibitor pifithrin-alpha is a potent agonist of the aryl hydrocarbon receptor

The tumor suppressor protein p53 is currently a target of emerging drug therapies directed toward neurodegenerative diseases, such as Alzheimer's and Parkinson's, and side effects associated with cancer treatments. Of this group of drugs, the best characterized is pifithrin-alpha, a small molecule that inhibits p53-dependent apoptosis through an undetermined mechanism. In this study, we have used a number of molecular approaches to test the hypothesis that pifithrin-alpha acts as an aryl hydrocarbon receptor (AhR) agonist and, in this manner, inhibits the actions of p53. Toward this end, we have found that pifithrin-alpha is a potent AhR agonist as determined by its ability to bind the AhR, induce formation of its DNA binding complex, activate reporter activity, and up-regulate the classic AhR target gene CYP1A1. However, examination of its ability to inhibit p53-mediated gene activation and apoptosis revealed that these actions occurred via an AhR-independent manner. The significance of this study is based on the fact that activation of the AhR is typically associated with an increase in phase I and phase II metabolizing enzymes and adverse biological events such as tumor promotion that may contribute to untoward effects of pifithrin-alpha. Hence, this work will aid in the future design of more specific members of this important class of p53 inhibitors for use in a clinical setting.