Current Pharmacogenomics - Volume 2, Issue 1, 2004

This review discusses the regulatory role of the human MDR1 multidrug transporter in the traffic of drugs and xenobiotics into the body as well as into certain organs and tissues (e.g. brain, germ cells, fetus). It also explores the relevance of single nucleotide polymorphisms (SNPs) within the MDR1 gene with respect to variations in MDR1 protein expression and function. In silico methods of SNP identification in the MDR1 gene are compared with experimentally determined SNP discovery methods, including direct sequencing and single-strand conformation polymorphism analyses. The distribution of the various SNPs in different ethnic groups is also discussed. We also provide an update on the current status of various association studies that have examined the role of MDR1 SNPs in altering plasma drug concentration, drug-induced side effects, drug response as well as susceptibility to disease, and the potential implications of these findings.

Canavan disease (CD) is an autosomal recessive disorder, caused by mutations in the aspartoacylase gene resulting enzyme deficiency. Patients with CD have accumulation of NAAG and NAA in the brain resulting elevated urinary NAAG and NAA. Aspartoacylase gene mutation in the mouse led to multiple genomic abnormalities. Pathophysiological processes implicated in CD include spongy degeneration of the brain possibly by the abnormal genes expression / metabolic levels of NAAG, NAA, aspartate, glutamate, glutamate transporter-EAAT4, GABA receptor-GABRA6 and GABA. In addition, high expression of cell death inducing agents includes serine proteinase inhibitor 2, caspase 11 and interleukin 1- beta. Osteoporosis is also an important consequence in the CD mouse. Each of these pathways offers potential therapeutic targets and pharmacological manipulation.

Single nucleotide polymorphisms (SNPs) represent the most common form of sequence variation in human DNA. With the completion of the human genome project, SNP genotyping is being undertaken in a large number of pharmacogenomic studies to identify variants associated with responses to specific drugs. The speed at which the goals of pharmacogenomics will be met depends on the development of a large set of SNP markers and a suite of high throughput genotyping methods. A number of methods for high throughput SNP genotyping have been developed. In most studies, a large number of SNPs must be genotyped in a large number of individuals, so the challenge for most laboratories is to find an affordable method that meets the dual requirements of high accuracy and high throughput. In this review, a number of robust genotyping methods currently in use are described, and estimated instrumentation and reagent costs are compared. Although no single genotyping method will suit all applications, the available technology allows pharmacogenomic studies of nearly any scale to be performed. However, advances are still required in genotyping technology to make whole genome genotyping rapid and cost-effective - a critical component of pharmacogenomic studies.

Epidemiological studies have suggested an association between an increased dietary intake of carotenoids and a reduced incidence of cancer, even if results from clinical trials indicated that β-carotene supplements do not protect against cancer and might actually increase the risk of lung cancer in smokers. Although several mechanisms by which carotenoids modulate cancer process have been reported, there are still conflicting opinions and little is known regarding their mechanisms of action at molecular levels. It appears that carotenoids can bring about a host of changes at the levels of both gene expression and protein activity in the cells. In particular, some evidences are shown that carotenoid molecules may interfere in cancer related molecular pathways and change the expression of many proteins involved in: 1) cell proliferation, differentiation, apoptosis and angiogenesis; 2) carcinogen detoxification; 3) DNA damage and repair; 4) immunosurveillance. Carotenoids seem to affect gene expression either directly by interference with the control apparatus of the gene expression machinery or by virtue of metabolites or metabolic conditions induced (hormonal status, cellular redox status, etc.) that, in turn, alter cell functions implicated in the cancer process. The suppression as well as the induction of cancer by carotenoids raises issues about possible doses of carotenoid administration, possible synergy as well as antagonistic interactions between carotenoids and other dietary components. Understanding the effects of carotenoids on cancer-related genetic pathways is fundamental, not only providing pathophysiological explanation for the development of cancer, but also improving strategies for cancer prevention.

Spermatogenesis involves action and interaction of several genes present both on the autosome and sex chromosomes. Protooncogene c-kit receptor is one such autosomal gene implicated with hematopoiesis, melanogenesis and spermatogenesis. A sizable body of literature is available on the regulatory role of this gene, its ligand “stem cell factor” and its functional conservation across the species. Sequences from the extracellular domains of c-kit cDNA show organizational uniqueness across the species conferring species specificity. Studies on fertile and infertile Brown Norway rats enabled identification of mutant mRNA transcript in the testis of infertile animals. These animals showed heavily regressed seminiferous tubules. No such mutant mRNA transcript was detected in the somatic tissues of infertile or normal animals. The mutant mRNA transcript was found in accordance with the regressed seminiferous tubules observed in the testicular histological section of the infertile rats. A perusal of literature and our own study suggest that alternate splicing of c-kit gene gives rise to multiple mRNA transcripts of which at least one is involved in control and regulation of fertility in conjunction with its ligand “stem cell factor” and perhaps other autosomal genes. In this article, we present a brief overview on the organization and expression of protooncogene c-kit receptor and its mutational status in Brown Norway rats (Rattus norvegicus). It is envisaged that information emerging from animal systems will facilitate the overall understanding of the phenomenon of fertility in the human as well.

The potential of pharmacogenomics has received widespread attention. The goals include identifying patients in whom a substantial response, or the absence of a response, to an individual drug can be anticipated; targets for drug therapy based on genetic polymorphisms involved in pathogenesis; and new opportunities for drug development. Diabetic (DM) nephropathy provides a useful model for exploring these issues since nephropathy occurs in 30-40% of patients, and diabetes is the most common cause of end-stage renal disease. Hyperglycemia and hypertension clearly contribute but do not explain fully the development of DM nephropathy. Family studies showed familial clustering in both type 1 and type 2 DM, with about a 3-fold increased risk in siblings if the proband had DM nephropathy. A search for candidate genes followed. The effectiveness of angiotensin converting enzyme (ACE) inhibitors and angiotensin receptor blockers in delaying the progression of DM nephropathy led to studies centering on polymorphisms of genes involving the renin-angiotensin system. These include the ACE, AGT, AT1R and renin genes. Despite an enormous number of studies, the results are still equivocal. An alternative approach is to use an intermediate phenotype to explore mechanisms. Our efforts have involved assessing the renal plasma flow response to ACE inhibition and angiotensin II receptor blockade in DM as an intermediate phenotype. The response provides a measure of angiotensin-dependent renal vasoconstriction, and thus, an index of intrarenal renin-angiotensin system activation, and shows promise as an effective tool in exploring the relation between gene polymorphisms and risk of disease.

NQO1 (NAD(P)H:quinone oxidoreductase-1) is a cytosolic flavoprotein that catalyses the two-electron reduction of endogenous and environmental quinones. NQO1 plays a prominent role in protecting cells from the toxic effects of quinones, oxidative stress and more recently, the stabilisation of p53. Paradoxically, NQO1 is a target for anti-cancer drug development as reduction of certain quinones can generate cytotoxic species. Polymorphic variants of NQO1 have been characterised, two of which are known to cause a significant reduction in NQO1 protein (609C>T and 465C>T termed NQO1*2 and NQO1*3,respectively). The incidence of the NQO1*2 allele is high in certain ethnic groups and the loss of NQO1 activity has potential implications for both the cancer susceptibility and the efficacy of quinone based anticancer drugs. Toxicity following exposure to benzene increases with lowered NQO1 activity and epidemiological evidence suggests that NQO1*2 is associated with an increased risk of developing certain types of cancer. Mitomycin C (MMC) is the major quinone based compound in routine clinical use and initial reports of reduced MMC efficacy in patients with the NQO1*2 allele are emerging. However, the role of NQO1 in metabolising MMC is complex and the relationship between NQO1 activity and response is controversial. It therefore remains to be determined whether NQO1 genotyping will significantly influence clinical decision making with respect to MMC therapy. Genotyping for NQO1 polymorphisms is however likely to play a significant role in the development and evaluation of other quinone based bioreductive drugs where NQO1 plays a more prominent role in drug activation.

Diversity in response to antihypertensive therapy is well-documented. Among many variables in the biological system, reasons include the genetic make-up of individuals. Although individual human genomes are 99.9% identical, the 0.1% difference predicts as many as three million polymorphisms. Some will affect protein expression or function, resulting in phenotypes affected for disease or with altered drug response. Pharmacogenomics focuses on the link between polymorphism in genes and variable response to drugs. The genetic approach to the study of the mechanisms underlying hypertension has led to the identification of some quantitative trait loci or genes that influence blood pressure regulation. An ultimate goal of pharmacogenomic knowledge is to advance beyond the current approach to antihypertensive drug therapy to more individualized approaches. Drugs that are more specific for the molecular characteristics of individual patients should contribute to greater efficacy and reduced toxicity. In this article, we review the pathophysiology of essential hypertension, the principles of its drug treatment, and those pharmacogenomic studies of antihypertensive treatment which, to our knowledge, have been published so far and which deals primarily with two aspects: the blood pressure lowering effect and the regression of left ventricular hypertrophy. Also, a selection of functional polymorphisms in potential candidate genes which have not yet appeared in pharmacogenomic studies of antihypertensive treatment but in various ways have been linked to hypertension and / or its related diseases / organ damages are discussed.