The genetic basis of variability in drug responses

Ethnic differences in cardiac potassium channel variants: implications for genetic susceptibility to sudden cardiac death and genetic testing for congenital long QT syndrome

OBJECTIVE

To determine the spectrum, frequency, and ethnic-specificity of channel variants in the potassium channel genes implicated in congenital long QT syndrome (LQTS) among healthy subjects.

SUBJECTS AND METHODS

Genomic DNA from 744 apparently healthy individuals-305 black, 187 white, 134 Asian, and 118 Hispanic--was subject to a comprehensive mutational analysis of the 4 LQTS-causing potassium channel genes: KCNQ1 (LQT1), KCNH2 (LQT2), KCNE1 (LQT5), and KCNE2 (LQT6).

RESULTS

Overall, 49 distinct amino acid-altering variants (36 novel) were identified: KCNQ1 (n = 16), KCNH2 (n = 25),KCNE1 (n = 5), and KCNE2 (n = 3). More than half of these variants (26/49) were found exclusively in black subjects. The known K897T-HERG and the G38S-min K common polymorphisms were identified in all 4 ethnic groups. Excluding these 2 common polymorphisms, 25% of black subjects had at least 1 nonsynonymous potassium channel variant compared with 14% of white subjects (P < .01).

CONCLUSIONS

To our knowledge, this study represents the first comprehensive determination of the frequency and spectrum of cardiac channel variants found among healthy subjects from 4 major ethnic groups. Defining the population burden of genetic variants in these critical cardiac ion channels is crucial for proper interpretation of genetic test results of individuals at risk for LQTS. This compendium provides a resource for epidemiological and functional investigation of variant effects on the repolarization properties of cardiac tissues, including susceptibility to lethal cardiac arrhythmias.

Using multiple drug exposure levels to optimize power in pharmacogenetic trials

Large-scale pharmacogenetic trials testing tens to hundreds of thousands of single-nucleotide polymorphisms (SNPs) will become possible in the near future given rapidly decreasing costs of genotyping. Devising optimal designs for these trials will be a significant challenge. The author demonstrates how the level of drug exposure may strongly affect the power to detect true associations between genetic polymorphisms and drug response. An analytic model of drug response is described that is used to simulate pharmacogenetic trials. Analytical and numerical sensitivity analyses are performed on the model to demonstrate possible exposure-sensitivity behaviors. This model shows that the power to detect an association can be a nonlinear, nonmonotonic function of drug exposure. This model is further investigated using two clinical trial designs. The conclusion is that trial designs that use more than one drug exposure or dose will have an increased likelihood of discovering statistically significant pharmacogenetic associations.

Cardiovascular pharmacogenetics in the SNP era

In the past pharmacological agents have contributed to a significant reduction in age-adjusted incidence of cardiovascular events. However, not all patients treated with these agents respond favorably, and some individuals may develop side-effects. With aging of the population and the growing prevalence of cardiovascular risk factors worldwide, it is expected that the demand for cardiovascular drugs will increase in the future. Accordingly, there is a growing need to identify the 'good' responders as well as the persons at risk for developing adverse events. Evidence is accumulating to indicate that responses to drugs are at least partly under genetic control. As such, pharmacogenetics - the study of variability in drug responses attributed to hereditary factors in different populations - may significantly assist in providing answers toward meeting this challenge. Pharmacogenetics mostly relies on associations between a specific genetic marker like single nucleotide polymorphisms (SNPs), either alone or arranged in a specific linear order on a certain chromosomal region (haplotypes), and a particular response to drugs. Numerous associations have been reported between selected genotypes and specific responses to cardiovascular drugs. Recently, for instance, associations have been reported between specific alleles of the apoE gene and the lipid-lowering response to statins, or the lipid-elevating effect of isotretinoin. Thus far, these types of studies have been mostly limited to a priori selected candidate genes due to restricted genotyping and analytical capacities. Thanks to the large number of SNPs now available in the public domain through the SNP Consortium and the newly developed technologies (high throughput genotyping, bioinformatics software), it is now possible to interrogate more than 200,000 SNPs distributed over the entire human genome. One pharmacogenetic study using this approach has been launched by GlaxoSmithKline to identify the approximately 4% of patients who are predisposed to developing a hypersensitivity reaction to abacavir, an anti-HIV agent. Data collected thus far on the HLA locus on chromosome 6 indicate that this approach is feasible. Extended linkage disequilibrium can be detected readily, even across several haplotype blocks, thus potentially reducing the number of SNPs for future whole-genome scans. Finally, a modest number of cases and controls appears to be sufficient to detect genetic associations. There is little doubt that this type of approach will have an impact on the way cardiovascular drugs will be developed and prescribed in the future.

Pharmacogenetics and clinical gastroenterology

Many drugs exhibit variable efficacy and toxicity. Pharmacogenetics explores the genetic underpinnings of variable drug response. Pharmacogenetic testing is beginning to enter the clinic and will have a significant impact on the practice of clinical gastroenterology. Thiopurine S-methyltransferase screening, which will likely become routine for thiopurine recipients, illustrates the promise and limitations of pharmacogenetics. Testing for variation in other drug metabolism pathways may also become important. Pharmacogenetics will complement but not replace traditional methods for choosing drugs and for selecting dosing regimens for narrow-therapeutic-index drugs.

Cardiovascular pharmacogenetics: on the way toward individually tailored drug therapy

G proteins are important mediators of hormone action in all cells of the human body. Therefore, functional polymorphisms in genes encoding G protein subunits are expected to have a marked influence upon cell activation and cardiovascular responses to hormones and drugs. The 825T allele of a common C825T polymorphism in the gene, GNB3, encoding the G beta 3 subunit, was found to be associated with increased intracellular signal transduction via G protein-coupled receptors. Originally defined as a candidate gene associated with an increased risk for essential hypertension, the 825T allele turns out to be an interesting marker in cardiovascular pharmacogenetics. Carriers of the 825T allele show an increased vasoconstriction in the skin microcirculation in response to noradrenaline, angiotensin II, and endothelin I. Coronary vasoconstriction is enhanced in 825T allele carriers in response to azepexol. On the other hand, some drugs like hydrochlorothiazide, clonidine, and endothelin receptor antagonist evoke increased effects in 825T allele carriers. It appears that the GNB3 C825T polymorphism could be an attractive marker to discriminate responders and nonresponders and might, therefore, represent an excellent candidate gene in cardiovascular pharmacogenetics.

The use of denaturing high-performance liquid chromatography (DHPLC) for the analysis of genetic variations: impact for diagnostics and pharmacogenetics

Over the past five years, denaturing high-performance liquid chromatography (DHPLC) has emerged as one of the most versatile technologies for the analysis of genetic variations. With the benefit of novel polymer chemistries used for separation, the accuracy, sensitivity, and the throughput of DHPLC for DNA and RNA analysis have greatly improved. DHPLC has been adopted in many laboratories for the screening of mutations and single-nucleotide polymorphisms (SNPs). The ability of DHPLC to detect known and unknown mutations simultaneously has put this technology at the forefront of genetic analysis for a wide variety of diseases. In addition, the high sensitivity of DHPLC combined with the accuracy of the heteroduplex analysis has allowed the development of applications beyond the scope of traditional sequencing or genotyping, e.g., the early detection of cancer. This article reviews the methods, which made DHPLC a widely used tool for diagnosis in molecular genetics and pharmacogenetics. The article provides an overview of current applications in these fields and points to novel applications in areas like epigenetics and the analysis of heteroplasmic mitochondrial DNA, in which DHPLC is becoming the leading technology.

Drugs that induce repolarization abnormalities cause bradycardia in zebrafish

BACKGROUND

Drug-induced QT prolongation and torsades de pointes remain significant and often unpredictable clinical problems. Current in vitro preclinical assays are limited by biological simplicity, and in vivo models suffer from expense and low throughput.

METHODS AND RESULTS

During a screen for the effects of 100 small molecules on the heart rate of the zebrafish, Danio rerio, we found that drugs that cause QT prolongation in humans consistently caused bradycardia and AV block in the zebrafish. Of 23 such drugs tested, 18 were positive in this initial screen. Poor absorption explained 4 of 5 false-negative results, as demonstrated by microinjection. Overall, 22 of 23 compounds that cause repolarization abnormalities were positive in this assay. Antisense "knockdown" of the zebrafish KCNH2 ortholog yielded bradycardia in a dose dependent manner confirming the effects of reduction of repolarizing potassium current in this model. Classical drug-drug interactions between erythromycin and cisapride, as well as cimetidine and terfenadine, were also reproduced.

CONCLUSION

This simple high-throughput assay is a promising addition to the repertoire of preclinical tests for drug-induced repolarization abnormalities. The genetic tractability of the zebrafish will allow the exploration of heritable modifiers of such drug effects.

Pharmacogenomic analysis of interferon receptor polymorphisms in multiple sclerosis

Multiple sclerosis (MS) is a common inflammatory disease of the central nervous system characterized by progressive neurological dysfunction. No curative therapy is currently available, and approximately 80-90% of afflicted individuals are ultimately disabled. Interferon beta (IFNbeta) has been shown to decrease clinical relapses, reduce brain disease activity, and possibly slow progression of disability. However, the overall effect of treatment is partial and a substantial number of patients are considered poor or nonresponders. For this report, we tested the pharmacogenomic effects of eight polymorphisms in the interferon receptor genes (IFNAR1 and IFNAR2) in a group of 147 patients undergoing open-label IFNbeta therapy. Overall, no significant differences in the distribution of responders and nonresponders, classified based on prospectively acquired primary and secondary clinical end points, were observed when stratified by any of the studied IFNAR gene polymorphisms. A trend detected with a single nucleotide polymorphism SNP 16469 (A/T) located at the third intron of the IFNAR1 gene, suggesting modest association with relapse-free status, will require confirmation in an independent data set. In addition, no significant association was observed of any of the IFNAR gene polymorphisms with susceptibility to MS, as studied by a family-based association analysis.

Safety considerations for statins

PURPOSE OF REVIEW

The hydroxymethyl glutaryl coenzyme A reductase inhibitors or statins offer important benefits for the large populations of individuals at high risk for coronary heart disease. These drugs have a good safety profile. Nevertheless, differences in physicochemical and pharmacokinetic properties between statins may translate into significant differences in long-term safety. This review focuses on long-term adverse effects related to statin use, namely hepatotoxicity and myopathy. Moreover, the most common drugs used in combination with statins in long-term therapies are analyzed in terms of possible drug/drug interactions affecting the safety of statins.

RECENT FINDINGS

The withdrawal of cerivastatin from the global market in 2001, because of severe cases of rhabdomyolysis, highlighted concerns regarding the safety of the entire class. Afterwards, the role of statins and their interactions with other drugs in precipitating this condition have been carefully reviewed. In approximately 60% of the total number of cases, statin-related rhabdomyolysis was found to be related to drug/drug interactions. Recently, all cases of fatal rhabdomyolysis associated with statin use have been reported to the US Food and Drug Administration. This has shown that fatal rhabdomyolysis among statin users is a rare event, the reporting rates being much less than one death per million prescriptions in the case of all statins except cerivastatin.

SUMMARY

The safety and tolerability of the available statins support their use as the first-line treatment of patients at high risk for coronary heart disease, since the clinical benefits greatly outweigh the small risk of myopathy. Nevertheless, clinicians should be aware of the adverse effects possibly related to statin therapy, particularly in patients at high risk for coronary heart disease and requiring long-term multiple-drug therapies.

Genetics of the immune response: identifying immune variation within the MHC and throughout the genome

With the advent of modern genomic sequencing technology the ability to obtain new sequence data and to acquire allelic polymorphism data from a broad range of samples has become routine. In this regard, our investigations have started with the most polymorphic of genetic regions fundamental to the immune response in the major histocompatibility complex (MHC). Starting with the completed human MHC genomic sequence, we have developed a resource of methods and information that provide ready access to a large portion of human and nonhuman primate MHCs. This resource consists of a set of primer pairs or amplicons that can be used to isolate about 15% of the 4.0 Mb MHC. Essentially similar studies are now being carried out on a set of immune response loci to broaden the usefulness of the data and tools developed. A panel of 100 genes involved in the immune response have been targeted for single nucleotide polymorphism (SNP) discovery efforts that will analyze 120 Mb of sequence data for the presence of immune-related SNPs. The SNP data provided from the MHC and from the immune response panel has been adapted for use in studies of evolution, MHC disease associations, and clinical transplantation.

Ethical perspectives on pharmacogenomic profiling in the drug development process

Pharmacogenomics, which is a field that encompasses the study of genetic polymorphisms that underlie individual differences in drug response, is rapidly advancing. The potential for the widespread use of pharmacogenomics in the drug development process merits an examination of its fundamental impact on clinical-trial design and practice. This article provides a critical analysis of some of the issues that pertain to pharmacogenomics in the drug development process. In particular, four areas will be discussed: clinical-trial design; subject stratification; some new social risks; and economic concerns. Recommendations are offered for addressing the issues that are discussed and anticipating the regulatory needs for pharmacogenomics-based trials.