The genetic basis of variability in drug responses

Lack of association between 71 variations located in candidate genes and response to acute haloperidol treatment

RATIONALE

The antipsychotic pharmacological treatment effectiveness and side effects are at least partially driven by the genetic personal background.

OBJECTIVES

In the present study, 71 genetic variations located in 21 candidate genes were investigated as modulators of the haloperidol efficacy and side effects in a sample of 101 acutely ill psychotic patients.

METHODS

Patients were assessed at days 0, 7, 14, 21, and 28 (Positive and Negative Syndrome Scale (PANSS) test) and days 1, 3, 7, 14, 21, and 28 (UKU, BAS, and ESRS tests). Haloperidol plasma levels were measured at the same timepoints.

RESULTS

None of the 71 variations were associated with response to treatment or with incidence of side effects passed a multiple testing threshold. A marginal association was detected between two haplotypes within the signal transducer and activator of transcription 4 gene and PANSS positive and dopamine beta-hydroxylase with PANSS negative scores (p = 0.004 and p = 0.008, respectively).

CONCLUSIONS

In conclusion, no major association was observed between the investigated variations and the efficacy profile of haloperidol.

Advances of molecular clinical pharmacology in gastroenterology and hepatology

During developmental age, differences in pharmacodynamic reactions to several drugs may reflect polymorphisms of genes encoding drug-transporting proteins, receptors, drug targets, and gene products, whose disturbed activity sometimes plays an important role in certain diseases. Administration of drugs with a narrow therapeutic index may quite easily be associated with changes in pharmacokinetics and development of adverse drug reactions, which occasionally may cause fatalities. In such cases, polypragmasy and resulting drug interactions may enhance effects of changes in drug-metabolizing enzymes' activities. Phenotyping and genotyping of patients slowly are finding their place in some therapeutic regimens used in clinical gastroenterology and hepatology. At present, some assays to measure, for example, thiopurine S-methyltransferase activity are already commercially available. Polymorphisms of CYP450 enzymes, interleukins, and altered gene expression play an important role in some patients' various gastrointestinal tract and liver diseases. Herbal drugs also affect proinflammatory and antiinflammatory cytokine and nitric oxide balance in the body. Therapeutic use of recombined proteins, such as infliximab, natalizumab, onercept, humanized antibody to integrin α-4 β-7, or IFN-β in some large-bowel diseases increased therapeutic efficacy. IFN-α used in the patients with chronic hepatitis C improved cellular immunity in these subjects and exerted antiviral activity. Practical application of progress in pharmacogenetics, pharmacokinetics, pharmacodynamics, and use of bioproducts in novel therapeutic regimens has opened therapeutic frontiers and increased clinical safety.

Pharmacogenetic screening of N-acetyltransferase 2, thiopurine s-methyltransferase, and 5,10-methylene-tetrahydrofolate reductase polymorphisms in Northwestern Mexicans

Specific information about the population pharmacogenetics can be the starting point to study the inheritance of these traits, to design individual drug therapy, and to develop new drugs rationally. Pharmacogenetic studies have been performed in some regions of Mexico, such as Central and Northeast, but this kind of study has not been conducted in the Northwest region so far. Here, we report the distribution of NAT2, TPMT, and MTHFR gene polymorphisms in Baja California, Mexico. We found that our population sample exhibits allele and genotype frequencies that are highly similar to those observed in Caucasian populations, although it should be noted that there are slight similarities with those determined in other populations. As allelic variants of drug-metabolizing enzymes are prevalent in our population, it is important to consider pharmacogenetic testing as part of the standard diagnostic protocols before medication.

The zebrafish: scalable in vivo modeling for systems biology

The zebrafish offers a scalable vertebrate model for many areas of biologic investigation. There is substantial conservation of genetic and genomic features and, at a higher order, conservation of intermolecular networks, as well as physiologic systems and phenotypes. We highlight recent work demonstrating the extent of this homology, and efforts to develop high-throughput phenotyping strategies suited to genetic or chemical screening on a scale compatible with in vivo validation for systems biology. We discuss the implications of these approaches for functional annotation of the genome, elucidation of multicellular processes in vivo, and mechanistic exploration of hypotheses generated by a broad range of 'unbiased' 'omic technologies such as expression profiling and genome-wide association. Finally, we outline potential strategies for the application of the zebrafish to the systematic study of phenotypic architecture, disease heterogeneity and drug responses.

The genetics of congestive heart failure

The heart failure syndrome is known to represent a final common pathway for a broad range of etiologies, but there is tremendous variation in the propensity to develop congestive heart failure after a given insult. This variation is thought to result in part from inherited differences in myocardial, vascular or systemic responses, but the nature of the underlying traits responsible ultimately for the development of heart failure has remained elusive. There has been limited progress in the genetic exploration of the key clinical phenotype itself: heart failure. In this article, the author attempts to place the results of genetic studies of cardiomyopathy in the broader context of the clinical syndrome of heart failure, highlighting some of the key questions for future study.

Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case

BACKGROUND

Mathematical modeling of biological networks is an essential part of Systems Biology. Developing and using such models in order to understand gene regulatory networks is a major challenge.

RESULTS

We present an algorithm that determines the smallest perturbations required for manipulating the dynamics of a network formulated as a Petri net, in order to cause or avoid a specified phenotype. By modifying McMillan's unfolding algorithm, we handle partial knowledge and reduce computation cost. The methodology is demonstrated on a glioma network. Out of the single gene perturbations, activation of glutathione S-transferase P (GSTP1) gene was by far the most effective in blocking the cancer phenotype. Among pairs of perturbations, NFkB and TGF-beta had the largest joint effect, in accordance with their role in the EMT process.

CONCLUSION

Our method allows perturbation analysis of regulatory networks and can overcome incomplete information. It can help in identifying drug targets and in prioritizing perturbation experiments.

Role of membrane transporters in the safety profile of drugs

It has increasingly been recognized that few molecules move across the cell membrane without the assistance of transporter proteins. Large superfamilies of transporter proteins have been identified in every living cell, including microorganisms and mitochondria. This report reviews the role of transporters in physiology and pharmacology, and identifies where this may have an impact on drug efficacy and toxicity. This new understanding will require a fresh appreciation of pharmacokinetics and drug effects, as the current paradigms are based largely on the assumption that drug molecules have a reasonable unrestricted permeability across membranes. Rather than just focusing on clearance changes and central compartment pharmacokinetics, it will become increasingly necessary to examine the peripheral tissue distribution of drugs to more accurately predict drug efficacy and toxicity.

A genomewide association study points to multiple loci that predict antidepressant drug treatment outcome in depression

CONTEXT

The efficacy of antidepressant drug treatment in depression is unsatisfactory; 1 in 3 patients does not fully recover even after several treatment trials. Genetic factors and clinical characteristics contribute to the failure of a favorable treatment outcome.

OBJECTIVE

To identify genetic and clinical determinants of antidepressant drug treatment outcome in depression.

DESIGN

Genomewide pharmacogenetic association study with 2 independent replication samples.

SETTING

We performed a genomewide association study in patients from the Munich Antidepressant Response Signature (MARS) project and in pooled DNA from an independent German replication sample. A set of 328 single-nucleotide polymorphisms highly related to outcome in both genomewide association studies was genotyped in a sample of the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study.

PARTICIPANTS

A total of 339 inpatients with a depressive episode (MARS sample), a further 361 inpatients with depression (German replication sample), and 832 outpatients with major depression (STAR*D sample).

MAIN OUTCOME MEASURES

We generated a multilocus genetic variable that described the individual number of alleles of the selected single nucleotide polymorphisms associated with beneficial treatment outcome in the MARS sample ("response" alleles) to evaluate additive genetic effects on antidepressant drug treatment outcome.

RESULTS

Multilocus analysis revealed a significant contribution of a binary variable that categorized patients as carriers of a high vs low number of response alleles in the prediction of antidepressant drug treatment outcome in both samples (MARS and STAR*D). In addition, we observed that patients with a comorbid anxiety disorder combined with a low number of response alleles showed the least favorable outcome.

CONCLUSION

These results demonstrate the importance of multiple genetic factors combined with clinical features in the prediction of antidepressant drug treatment outcome, which underscores the multifactorial nature of this trait.

Pharmacogenomics of antidepressant drugs

While antidepressant pharmacotherapy is an effective treatment of depression, it is still hampered by the slow onset of appreciable clinical improvement and a series of side effects. Moreover, a substantial group of patients does not achieve remission or fails to respond at all. One possible source accounting for these variations in treatment outcome are genetic differences. In recent years a number of pharmacogenetic studies on antidepressant drugs have been published. This manuscript summarizes findings related to the pharmacogenetics of genes involved in the pharmacokinetics as well as pharmacodynamics of antidepressants to date. Illustrated by examples from current candidate gene- and whole genome association studies, this manuscript critically discusses aspects of pharmacogenetic studies in antidepressant response related to study design and clinical relevance.

A network medicine approach to human disease

High-throughput interaction discovery initiatives are providing thousands of novel protein interactions which are unveiling many unexpected links between apparently unrelated biological processes. In particular, analyses of the first draft human interactomes highlight a strong association between protein network connectivity and disease. Indeed, recent exciting studies have exploited the information contained within protein networks to disclose some of the molecular mechanisms underlying complex pathological processes. These findings suggest that both protein-protein interactions and the networks themselves could emerge as a new class of targetable entities, boosting the quest for novel therapeutic strategies.

Common genetic variation in six lipid-related and statin-related genes, statin use and risk of incident nonfatal myocardial infarction and stroke

OBJECTIVE

Genetic polymorphisms are associated with lipid-lowering response to statins, but generalizeability to disease endpoints is unclear. The association between 82 common single nucleotide polymorphisms (SNPs) in six lipid-related or statin-related genes (ABCB1, CETP, HMGCR, LDLR, LIPC, NOS3) and incident nonfatal myocardial infarction (MI) and ischemic stroke was analyzed according to current statin use and overall in a population-based case-control study (856 MI, 368 stroke, 2686 controls).

METHODS

Common SNPs were chosen from resequencing data using pairwise linkage disequilibrium. Gene-level analyses (testing global association within a gene) and SNP-level analyses (comparing the number of observed vs. expected associations across all genes) were performed using logistic regression, setting nominal statistical significance at P value of less than 0.05.

RESULTS

No gene-level interactions with statin use on MI or stroke were identified. Across all genes, two SNP-statin interactions on MI were observed (one ABCB1, one LIPC) and five interactions on stroke (one CETP, four LIPC). The strongest SNP-statin interaction was for synonymous CETP SNP rs5883 on stroke (P=0.008). Gene-level associations were present for LIPC and MI (P=0.026), but not other genes or outcomes. SNP-level associations included three SNPs with MI (one LDLR, two LIPC) and two SNPs with stroke (one CETP, one LDLR). The number of observed SNP associations was no greater than expected by chance.

CONCLUSION

Several potential novel associations or interactions of SNPs in ABCB1, CETP, LDLR, and LIPC with MI and stroke were identified; however, our results should be regarded as hypothesis generating until corroborated by other studies.

Single nucleotide polymorphisms and haplotype of four genes encoding cardiac ion channels in Chinese and their association with arrhythmia

BACKGROUND

Many studies revealed that variations in cardiac ion channels would cause cardiac arrhythmias or act as genetic risk factors. We hypothesized that specific single nucleotide polymorphisms in cardiac ion channels were associated with cardiac rhythm disturbance in the Chinese population.

METHOD

We analyzed 160 nonfamilial cardiac arrhythmia patients and 176 healthy individuals from which 81 individuals were selected for association study, and a total of 19 previously reported SNPs in four cardiac ion channel genes (KCNQ1, KCNH2, SCN5A, KCNE1) were genotyped.

RESULTS

The frequency of KCNQ1 1638G>A, as well as the haplotype harboring KCNQ1 1638A, KCNQ1 1685 + 23G and 1732 + 43T (haplotype AGT) was significantly higher in healthy controls than in arrhythmia patients. This finding implicated that this haplotype (AGT) might be a protective factor against arrhythmias.

CONCLUSIONS

Our study provided important information to elucidate the effect of SNPs of cardiac ion channel genes on channel function and susceptibility to cardiac arrhythmias in Chinese population.

Contribution of allelic variations to the phenotype of response to antidepressants and antipsychotics

Individualized medicine through molecular pharmacogenetics is one of the major future goals in clinical medicine. In psychopharmacology, pharmacogenetics became an expanding research component. Major research results were already attained: first, it is now feasible to predict a major proportion of the interindividual variation of plasma levels of most antidepressants and antipsychotics by using the DNA-sequence variation in genes for crucial CYP P450-enzymes as CYP2D6. Second, it is now possible to relate serious side effects (tardive dyskinesia, weight gain) of antipsychotics to specific genetic variants of genes for target proteins. Third, a long list of mainly functional variants in target protein genes was explored for their predictive power for the beneficial and adverse treatment outcome. Although specific results transferable into clinical practice were not yet obtained in this respect, the proof of principle could be demonstrated.

Frequency of CYP2C9 genotypes among Omani patients receiving warfarin and its correlation with warfarin dose

OBJECTIVES

This study was conducted to determine the frequency of CYP2C9 alleles in Omani patients receiving warfarin and to correlate genotyping data with warfarin dosage. The Omani population has Asian and African ethnicities.

METHODS

CYP2C9 genotypes were determined by the polymerase chain reaction restriction fragment length polymorphism method. Non-parametric Kruskal-Wallis test was used to compare groups of continuous data for significance differences.

RESULTS

Genotyping data showed that 12.7 and 5.8% of the samples were heterozygous for the CYP2C9*2 and CYP2C9*3 alleles, respectively. The CYP2C9*2 allele frequency was 0.074 in our population. It was 0.029 for CYP2C9*3.

CONCLUSION

This is the first report on the presence of CYP2C9*2 allele homozygocity in any Asian or African population.

Determination of CYP2D6, CYP2C9 and CYP2C19 genotypes with Tag-It mutation detection assays

Cytochrome P450 (CYP) genotyping can be used to prospectively identify individuals at risk for adverse drug reactions or therapeutic failure due to altered drug metabolism. Based on the specific CYP(s) affected, individuals may require less or more of a particular drug than people with unaffected CYP-mediated metabolism, or may be best managed by avoiding certain drugs entirely. Here we evaluated the Tag-It CYP mutation detection reagents (Tm Bioscience Corp.). As these reagents, based on a universal bead array, detect more than 20 clinically significant variants common to different ancestries, it was important to consider DNA from genetically diverse populations. Thus, we also report CYP2D6, CYP2C9 and CYP2C19 genotypes for DNA available through the Coriell Institute for Medical Research (NJ, USA). These samples represent individuals from Caucasian, Japanese, Chinese, Southeast Asian, African-American and Middle Eastern ancestry, and provide an excellent resource for evaluating and validating CYP genotyping methods. Using these samples, the Tag-It mutation detections assays reliably provided genotypes for CYP2D6, CYP2C9 and CYP2C19. The CYP2C9 and CYP2C19 assays were particularly robust and were easily implemented in our clinical laboratory. The CYP2D6 assay was somewhat less robust and could be improved by associating the 2850C>T variant with a specific allele, as well as by discriminating the allele affected when gene duplication is detected.

Sudden cardiac death in Andersen-Tawil syndrome

Andersen-Tawil syndrome (ATS) is an autosomal dominant or sporadic disorder characterized by periodic paralysis, dysmorphic features, and ventricular arrhythmias. Although ventricular tachycardia burden is quite high sudden cardiac death in ATS is rare. We describe a case with sudden cardiac death due to electrical storm a few days after ICD implantation in KCNJ2 mutation-negative ATS.

Identifying drugs needing pharmacogenetic monitoring in a Korean hospital

PURPOSE

A decision matrix for identifying drugs for which pharmacogenetic drug monitoring (PDM) provides the greatest benefit in a Korean setting is described.

SUMMARY

We developed a decision matrix including the ethnic frequency of clinically relevant polymorphic cytochrome P-450 (CYP) enzymes, and the metabolic profiles and adverse drug reactions of drugs. Using the developed decision matrix based on the population allele frequencies of CYP enzymes, we identified potential candidates for PDM among the most commonly used drugs at Seoul National University Hospital (SNUH). Collectively, 17 of these drugs were largely metabolized by at least one polymorphic CYP enzyme. Pharmacogenetic information was used to identify CYP2C9, CYP2C19, and CYP2D6 as the major CYP enzymes of clinical importance for pharmacologic effect and safety in Koreans. The frequencies of poor and intermediate metabolizers among Koreans were 0% and 2.3-12% for CYP2C9, 12% and 42% for CYP2C19, and 0.44% and 28% for CYP2D6, respectively. The frequency of ultrarapid metabolizers of CYP2D6 was 2.28%. The decision matrix and pharmacogenetic information were used to identify seven drugs for PDM: warfarin, glimepiride, diazepam, amitriptyline, nortriptyline, codeine, and oxycodone. This approach can be applied to other institutional hospitals or other ethnic populations and would be helpful for advancing pharmacy practice. Further work is required to assess the practical and potential clinical relevance of pharmacogenetic variations on drugs of interest before the implementation of PDM.

CONCLUSION

A decision matrix helped identify drugs for which PDM provides the greatest potential benefit at one Korean hospital.

Pharmacogenetics and diseases of the colon

PURPOSE OF REVIEW

The deciphering of the human genome sequence has enabled the identification of genetic polymorphisms that are responsible for inter-individual variation in the response to drug therapy. This field is referred to as pharmacogenetics. We review the impact of pharmacogenetics on therapy in diseases of the colon using three common variant enzyme systems as examples.

RECENT FINDINGS

Many enzyme systems impact the treatment of diseases of the colon. Examples include thiopurine S-methyltransferase, dihydropyrimidine dehydrogenase and flavin monooxygenase 3. They affect the management of inflammatory bowel disease, colorectal cancer and the chemoprevention of colorectal adenoma by influencing the metabolism of their respective substrates, azathioprine/6-mercaptopurine, 5-fluorouracil and sulindac. Recent studies have implicated the significance of genetic polymorphisms in each of the three drug-metabolizing enzymes, which impacts on the therapeutic outcome of the stated diseases. These studies highlight the potential role of pharmacogenetics in the design of a therapeutic plan which would increase efficacy and limit toxicity.

SUMMARY

Pharmacogenetics of drug-metabolizing systems continues to gain significance in the drug therapy of a variety of disease states including those of the gastrointestinal tract.

Plasma cholesterol is hyperresponsive to statin in ABCG5/ABCG8 transgenic mice

Interindividual variation exists in response to statin therapy. It has been hypothesized that subjects with higher baseline cholesterol synthesis rates are more sensitive to statins. To directly test this hypothesis, mice overexpressing the heterodimeric ATP-binding cassette (ABC) transporter G5/G8 (G5G8(Tg) mice) were treated with lovastatin because they have a compensatory increase in cholesterol biosynthesis as a result of increased cholesterol excretion into bile and feces. As expected, lovastatin treatment did not alter plasma and hepatic cholesterol levels in wild-type mice. Interestingly, this treatment significantly reduced plasma concentration and hepatic content of cholesterol by 42% and 17.3%, respectively, in the statin-treated versus untreated G5G8(Tg) mice despite a greater feedback upregulation of genes in the pathway of cholesterol biosynthesis in the lovastatin-treated G5G8(Tg) mice. The reduced plasma cholesterol concentration is unlikely to be attributed to LDL and HDL receptors because the protein levels of both receptors remained unchanged. Surprisingly, statin treatment resulted in an increase in biliary cholesterol concentration, which was associated with an upregulation in hepatic mRNA and protein levels of ABCG5 and ABCG8, and in hepatic mRNA levels of Niemann-Pick C1-Like 1 (NPC1L1), a gene that is required for intestinal cholesterol absorption. In conclusion, mice with higher endogenous cholesterol synthesis rates are more sensitive to statin. A synergistic hypocholesterolemic effect could be potentially achieved in humans by simultaneously inhibiting cholesterol biosynthesis and promoting ABCG5/ABCG8-mediated cholesterol excretion.

Relocating health governance: personalized medicine in times of 'global genes'

To date, governance questions related to personalized medicine - the consideration of the genetic and genomic determinants of varying drug response in patients - have been primarily addressed in terms of ethical implications. However, an analysis of the governance of personalized medicine should reach further. At present, governance issues arise in the context of an ongoing dispersion of national regulatory power. Due to the growing complexity of society, it has become impossible to govern society from a single center or by means of a single privileged governance mechanism. Governing increasingly includes the active participation of nongovernmental and individual actors by means of creating informal norms of conduct. Personalized medicine, due to its core concepts, fosters the emergence of new alliances (private and public, regional and global, for-profit and for-health) and thereby bears the promise to bridge some traditional dichotomies. Much rather than the quest for individualized drugs, it is this characteristic of personalized medicine that attracts so much attention from outside the medical and life science field.

Pharmacogenomics

So far no pharmacogenetic/genomic study has been conducted specifically for anxiety disorders. Some of the presented results, however, do pertain to such disorders. For example, pharmacokinetic aspects of antidepressant drug therapy likely also apply to patients with anxiety disorders, and several genetic polymorphisms in the cytochrome P450 (CYP) gene family and drug transporter molecules, such as the multidrug resistance (MDR) gene type 1, have been reported to influence the pharmacokinetics of antidepressant drugs. At this stage of pharmacogenomics research, it is difficult to interpret the relevance of pharmacodynamic-genetic association studies conducted in depressed patients for anxiety disorders. A number of studies have reported an influence of polymorphisms of genes mostly in the serotonergic pathway on the response to antidepressant drugs in patients suffering from depression. In order to know whether they can be extrapolated to patients with anxiety disorders, clinical studies are warranted. Despite all the shortcomings of the currently available pharmacogenetic studies, this field holds great promise for the treatment of anxiety disorders. In the future, psychiatrists may be able to base treatment decisions (i.e., the type and dose of prescribed drug) on more objective parameters than only the diagnostic algorithms used now. This will limit unwanted side effects and adverse drug reactions, and could reduce time to response, resulting in a more individualized pharmacotherapy.

Statin response and pharmacokinetics variants

Despite statin therapy being effective in the primary and secondary prevention of coronary heart disease, the benefit of treatment varies between individuals. Interindividual variations in pharmacokinetics play a central role in the cause of variability of drug disposition, and, in turn, the drug's clinical efficacy. Exploring genetic variations that influence pharmacokinetics may lead clinicians to apply the most efficient and safe drug therapy. So far, variants in eight candidate genes related to pharmacokinetics of statins have been investigated as the potential determinant of drug responsiveness or adverse event risk. All reported data remains inconclusive, but it has been suggested that combined analysis of more than two different polymorphisms, or a combination of genetic association and studies using in vitro recombinant expression techniques, may be more informative in predicting the specific phenotype of a genetic variant. Future studies using these approaches could provide more striking evidence, which may be sufficient to justify genetic analysis regarding pharmacokinetic variants in the clinical practice of statin therapy.

Implications of genetic polymorphisms in drug transporters for pharmacotherapy

Drug transporters are increasingly recognized as a key determinant of drug disposition and response. It is now widely appreciated that expression of the ATP-dependent efflux transporter, MDR1 (ABCB1, P-glycoprotein), in organs such as the gastrointestinal tract, liver and kidney significantly alters the extent of drug absorption and excretion. Moreover, expression of MDR1 at the level of the blood-brain barrier limits the entry of many drugs into the central nervous system. Given such an important role of MDR1 in the drug disposition process, it is not surprising to see increasing focus on the role of single nucleotide polymorphisms (SNPs) in this transporter as a potential determinant of interindividual variability in drug disposition and pharmacological response. However, drug transport is often the result of the concerted action of efflux and uptake pumps located both in the basolateral and apical membranes of epithelial cells. A growing list of membrane-spanning proteins involved in the in- or outward transport of a large variety of drugs has been recognized and characterized over the past few years in almost all tissues, including organic anion and cation transporters (OAT, OCT, solute carrier family SLC22A), organic anion transport proteins (OATP, solute carrier family SLCO, formerly SLC21A), and MRPs (ABCCs), other members of the ATP-binding cassette family. We are just beginning to appreciate their role for drug delivery and disposition and the contribution of genetic polymorphisms in these transport proteins to interindividual variability in the efficacy and safety for pharmacotherapy. This review summarizes the consequences of inherited differences in drug transport for pharmacotherapy. With the main focus on ABCB1, an update of recent advances is given and clinically relevant examples are used to illustrate how heritable differential drug transport can help to explain individual variability in drug response. The pharmacogenetics of other transporters is briefly introduced.

Cholestanol: A serum marker to guide LDL cholesterol-lowering therapy

Statins have been the mainstay of lipid-lowering therapy since their introduction. However, as lower LDL cholesterol targets are sought, adjunct therapies are becoming increasingly important. Few patients reach new targets with statin monotherapy. We propose that the cholestanol:cholesterol ratio can be used to guide lipid-lowering therapy and result in greater numbers of patients reaching target LDL cholesterol. By determining whether a patient is mainly a synthesizer or absorber of cholesterol, customized regimens can be used and are expected to improve patient outcomes and minimize costs of treatment.

Cardiac Na+ channels as therapeutic targets for antiarrhythmic agents

There are many factors that influence drug block of voltage-gated Na+ channels (VGSC). Pharmacological agents vary in conformation, charge, and affinity. Different drugs have variable affinities to VGSC isoforms, and drug efficacy is affected by implicit tissue properties such as resting potential, action potential morphology, and action potential frequency. The presence of polymorphisms and mutations in the drug target can also influence drug outcomes. While VGSCs have been therapeutic targets in the management of cardiac arrhythmias, their potential has been largely overshadowed by toxic side effects. Nonetheless, many VGSC blockers exhibit inherent voltage- and use-dependent properties of channel block that have recently proven useful for the diagnosis and treatment of genetic arrhythmias that arise from defects in Na+ channels and can underlie idiopathic clinical syndromes. These defective channels suggest themselves as prime targets of disease and perhaps even mutation specific pharmacological interventions.

Pharmacogenomics and antidepressant drugs

While antidepressant pharmacotherapy is an effective treatment of depression, it still is hampered by a delayed time of onset of clinical improvement and a series of side effects. Moreover, a substantial group of patients has only limited response or fails to respond at all. One source accounting for these variations are genetic differences as currently analysed by single nucleotide polymorphisms (SNP) mapping. In recent years a number of pharmacogenetic studies on antidepressant drugs have been published. So far they mostly focused on metabolizing enzymes of the cytochrome P450 (CYP) families and genes within the monoaminergic system with compelling evidence for an effect of CYP2D6 polymorphisms on antidepressant drug plasma levels and of a serotonin transporter promoter polymorphism on clinical response to a specific class of antidepressants, the selective serotonin reuptake inhibitors. It is clear, however, that other candidate systems have to be considered in the pharmacogenetics of antidepressant drugs, such as neuropeptidergic systems, the hypothalamus-pituitary adrenal (HPA) axis and neurotrophic systems. There is recent evidence that polymorphisms in genes regulating the HPA axis have an important impact on response to antidepressants. These studies mark the beginning of an emerging standard SNP profiling system that ultimately allows identifying the right drug for the right patient at the right time.

Gene mapping strategies for complex disease and drug response

The identification of genetic variants involved in disease susceptibility and response to drugs through the use of statistical and epidemiological approaches is a potentially powerful methodology for uncovering causal relationships in human disease and its treatment. Here we introduce and compare the application of genetics in these two fields of research.:

Statin pharmacogenomics: what have we learned, and what remains unanswered?

PURPOSE OF REVIEW

Statins are widely prescribed and are established as first-line therapy for the primary and secondary prevention of coronary heart disease. Response to treatment varies considerably from person to person; however, inherited traits (genetic variability) may play a central role in this inter-individual variation. The purpose of this review is to summarize recent progress in the research for exploring genetic determinants of clinical efficacy and safety of statin therapy.

RECENT FINDINGS

In addition to 41 previous studies of 19 genes, the results of 17 pharmacogenomic studies investigating the relationship between common genetic variants and response to statin therapy in terms of lipid responses, clinical outcomes, and adverse events have been reported since January 2004 - 15 candidate genes related to pharmacodynamics and three to pharmacokinetics of statins. These reported data suggest that genetic variations influencing intestinal cholesterol absorption, cholesterol production, and lipoprotein catabolism may all play a role in modulating responsiveness, as well as genes involved in drug metabolism of statins. They also suggest that combined analysis of multiple variants in several genes, all of which have possible functional relations, is more likely to give significant results, especially when being performed with a larger number of participants.

SUMMARY

Pharmacogenomic studies of statin therapy will provide a better picture as to who is most likely and least likely to benefit from treatment, which results in more individualized management of coronary artery disease.

Pharmacogenomics of statin responsiveness

Statins are widely prescribed and are established as first-line therapy for the primary and secondary prevention of coronary artery disease. However, the benefit of treatment varies between patients. Genetic variation can contribute to interindividual variations in clinical efficacy of drug therapy, and significant progress has been made in identifying common genetic polymorphisms that influence responsiveness to statin therapy. To date, >30 candidate genes related to pharmacokinetics and pharmacodynamics of statins have been investigated as potential determinants of drug responsiveness in terms of low-density lipoprotein cholesterol lowering. Genetic variation at gene loci that affect intestinal cholesterol absorption include apolipoprotein (apo) E; adenosine triphosphate-binding cassette transporter G5 and G8; cholesterol production, such as 3-hydroxy-3-methylglutaryl coenzyme A reductase; and lipoprotein catabolism, such as apoB and the low-density lipoprotein receptor, all may play a role in modulating responsivesness as well genes involved in metabolism of statins such as cytochrome P450. However, there is considerable variation in results reported, and the data suggest that combined analysis of multiple genetic variants in several genes, all of which have possible functional significance, is more likely to give significant results than single gene studies in small sample populations. In the future, pharmacogenomic studies with a greater number of participants (>2,000 participants) should provide a better picture as to who is most likely and who is least likely to benefit from statin therapy.

TaqMan applications in genetic and molecular toxicology

Quantification of nucleic acids has become a common procedure in many toxicology laboratories. Among the technologies that accomplish this is the fluorogenic 5'-nuclease assay, commonly known as TaqMan. Three TaqMan applications for genetic and molecular toxicology are presented in this article: quantification of gene expression, detection of genetic polymorphisms, and quantification of chromosomal DNA deletions. Of these, quantification of gene expression is the most widely used, and established TaqMan as a benchmark technology for nucleic acid quantification. Two additional applications, polymorphism detection and quantification of DNA deletions, demonstrate the flexibility and quantitative strengths that make TaqMan so powerful, including high precision, excellent sensitivity, and broad linear dynamic range. These and similar applications improve our ability to investigate genetic and molecular dimensions of toxicological phenomena, and have promoted the widespread use of TaqMan in toxicology departments in the pharmaceutical industry. In addition to presenting these applications, the authors discuss some of the challenges of integrating TaqMan and other new technologies into the drug development process.

Spectrum and prevalence of cardiac sodium channel variants among black, white, Asian, and Hispanic individuals: implications for arrhythmogenic susceptibility and Brugada/long QT syndrome genetic testing

OBJECTIVES

The purpose of this study was to determine the prevalence and spectrum of nonsynonymous polymorphisms (amino acid variants) in the cardiac sodium channel among healthy subjects.

BACKGROUND

Pathogenic mutations in the cardiac sodium channel gene, SCN5A, cause approximately 15 to 20% of Brugada syndrome (BrS1), 5 to 10% of long QT syndrome (LQT3), and 2 to 5% of sudden infant death syndrome.

METHODS

Using single-stranded conformation polymorphism, denaturing high-performance liquid chromatography, and/or direct DNA sequencing, mutational analysis of the protein-encoding exons of SCN5A was performed on 829 unrelated, anonymous healthy subjects: 319 black, 295 white, 112 Asian, and 103 Hispanic.

RESULTS

In addition to the four known common polymorphisms (R34C, H558R, S1103Y, and R1193Q), four relatively ethnic-specific polymorphisms were identified: R481W, S524Y, P1090L, and V1951L. Overall, 39 distinct missense variants (28 novel) were elucidated. Nineteen variants (49%) were found only in the black cohort. Only seven variants (18%) localized to transmembrane-spanning domains. Four variants (F1293S, R1512W, and V1951L cited previously as BrS1-causing mutations and S1787N previously published as a possible LQT3-causing mutation) were identified in this healthy cohort.

CONCLUSIONS

This study provides the first comprehensive determination of the prevalence and spectrum of cardiac sodium channel variants in healthy subjects from four distinct ethnic groups. This compendium of SCN5A variants is critical for proper interpretation of SCN5A genetic testing and provides an essential hit list of targets for future functional studies to determine whether or not any of these variants mediate genetic susceptibility for arrhythmias in the setting of either drugs or disease.

Pharmacogenetics of HMG-CoA reductase inhibitors: exploring the potential for genotype-based individualization of coronary heart disease management

Despite the benefit of statin therapy in the prevention of coronary heart disease, a considerable inter-individual variation exists in its response. It is well recognized that genetic variation can contribute to differences in drug disposition and, consequently, clinical efficacy at the population level. Pharmacogenetics, exploring genetic polymorphisms that influence response to drug therapy, may one day allow the clinician to customize treatment strategies for patients in order to improve the success rate of drug therapies. To date, 41 studies have investigated the relationships between common genetic variants and response to statin therapy in terms of lipid effects and clinical outcomes; 16 candidate genes involved in lipoprotein metabolism and 3 in pharmacokinetics. APOE is the most extensively studied locus, and absolute difference in LDL cholesterol reduction across genotypes remained 3-6%. Moreover, none of the associations was striking enough to justify genetic analysis in clinical practice. Reported data have suggested that larger studies (>1000 participants) or combination analyses with >2 different polymorphisms would enable us to find clinically or biologically meaningful difference, which could be assumed as >10% absolute difference, and that genes influencing cholesterol biosynthesis in the liver, such as ABCG5/G8, CYP7A1, HMGCR, would be good candidates for future studies.

Polymorphism screening in the cardiac K+ channel gene KCNA5

BACKGROUND

Common deoxyribonucleic acid polymorphisms that modulate normal cardiac electrophysiologic characteristics have previously been identified in long QT syndrome disease genes. In this study we screened an additional gene encoding the cardiac potassium channel KCNA5 (underlying I(Kur)) in 3 ethnic groups and evaluated the functional consequences of the variants identified.

METHODS

The coding region was screened by single-stranded conformational polymorphism analysis and direct sequencing, and nonsynonymous variants were studied by patch-clamping transfected Chinese hamster ovary cells. Results Five synonymous and 6 nonsynonymous polymorphisms were found in KCNA5. None of these polymorphisms was present in greater than 7% of alleles screened or in all 3 ethnic groups. Expression of the nonsynonymous KCNA5 variants revealed normal gating. However, 2 variants (P532L and R578K, both in the C-terminus) were resistant to block by the prototypical inhibitor quinidine; the concentration required to block I(Kur) by 50% (IC(50)) was 8.4 micromol/L for wild type versus 54 micromol/L for R578K and 133 micromol/L for P532L (both P < .0001, versus wild type).

CONCLUSION

KCNA5 displays little variability in its coding region. C-terminal KCNA5 variants displayed near-normal gating but striking resistance to drug block; thus these pharmacogenomic studies have identified a heretofore-unappreciated role of this region as a modulator of channel sensitivity to drugs. Resistance to I(Kur) blockers may be genetically determined.

Pharmacogenetics of methotrexate

Methotrexate (MTX) has proven efficient in the treatment of a number of malignancies, as well as non-malignant disorders characterized by a rapid cellular growth. Yet some patients might develop resistance, while others could have toxic side effects. MTX achieves its cytotoxicity through the inhibition of folate-dependent enzymes, suggesting that the genes controlling their activity or the levels of folate cofactors can modulate drug efficacy and, thus, the sensitivity of a patient to MTX. Indeed, several studies, conducted mostly in leukemia and rheumatoid arthritis patients, have addressed the potential for tailoring MTX therapy based on a patient's genetics. Several genetic variants have been shown to have a predictive role, among which the most frequently studied are those of methylenetetrahydrofolate reductase and thymidylate synthase genes. The other candidates, as well as gene-gene interactions, which may be even more important for the prediction of disease outcomes than the individual gene effects, are also briefly discussed.

Pharmacogenetics - five decades of therapeutic lessons from genetic diversity

Physicians have long been aware of the subtle differences in the responses of patients to medication. The recognition that a part of this variation is inherited, and therefore predictable, created the field of pharmacogenetics fifty years ago. Knowing the gene variants that cause differences among patients has the potential to allow 'personalized' drug therapy and to avoid therapeutic failure and serious side effects.

Genotyping with TaqMAMA

TaqMAMA combines the quantitative strengths of TaqMan with the allele-specific PCR of MAMA. In this article we develop TaqMAMA as a technique for screening human DNA samples for known genetic polymorphisms. In the first set of experiments, plasmids that model all types of genetic polymorphisms were used to understand the relationship between TaqMAMA primer/template mismatches and their strength of allelic discrimination. These data can be used to improve allelic discrimination of other primer extension genotyping methodologies through directed use of nucleotide mismatches. We used the data to derive a guide for TaqMAMA primer design and DNA strand selection for TaqMAMA genotyping assays. The guide was then used to develop assays for 11 known and novel human genetic polymorphisms. Genotypes were assigned quickly and accurately in all cases. TaqMAMA genotyping assays require minimal development time, have a high probability of success, produce reliable data that are straightforward to analyze, and are very cost-competitive.

Aryl hydrocarbon receptor polymorphisms and dioxin resistance in Atlantic killifish (Fundulus heteroclitus)

The aryl hydrocarbon receptor (AHR) gene encodes a ligand-activated transcription factor through which planar halogenated aromatic hydrocarbons (HAHs) such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) as well as polynuclear aromatic hydrocarbons (PAHs) cause altered gene expression and toxicity. To understand the role of AHR genetic variability in differential sensitivity to HAHs and PAHs, we are currently studying a population of the teleost Fundulus heteroclitus (Atlantic killifish) that has evolved genetic resistance to the toxic and biochemical effects of these compounds. Here, we report that the killifish AHR1 locus is highly polymorphic and that the frequencies of the major allele types differ between dioxin-sensitive and dioxin-resistant populations. Twenty-five single nucleotide polymorphisms (SNPs), nine of which are non-synonymous, were identified in the AHR1 coding sequence. Seven identified alleles were assigned to three groups, designated AHR1*1, AHR1*2 and AHR1*3. AHR1*1 alleles were under-represented in a population of dioxin- and polychlorinated biphenyl (PCB)-resistant fish from a PCB-contaminated Superfund site (New Bedford Harbor, Massachusetts, USA) compared to dioxin-sensitive fish from a less contaminated reference site (Scorton Creek, Massachusetts, USA). To determine the possible role of these AHR1 variants in differential HAH sensitivity, we expressed representative variant proteins from the two most divergent allelic groups (AHR1*1 and AHR1*3) by in-vitro transcription and translation and assessed their functional properties. AHR1*1A and AHR1*3A proteins displayed similar binding capacities and affinities for [H]TCDD. In transient transfection assays using mammalian cells, AHR1*1A and AHR1*3A exhibited similar abilities to support TCDD-dependent transactivation of a luciferase reporter gene under control of AHR-responsive enhancer elements. We discuss the possibility of other functional differences in AHR1 variants or their interaction with other killifish loci (AHR2, AHRR) that may contribute to differences in dioxin sensitivity.

Genomic and non-genomic interactions of PPARalpha with xenobiotic-metabolizing enzymes

The hypolipidemic properties of fibrates, synthetic activators of the nuclear receptor, peroxisome proliferator-activated receptor alpha (PPARalpha), have been studied extensively. Recent observations indicate, however, that PPARalpha also functions as a regulator of endobiotic and xenobiotic metabolism in rodents and humans. Activators of PPARalpha affect xenobiotic-metabolizing enzymes (XMEs) at different levels. At the genomic level, the expression of numerous cytochrome P450 (CYP) and phase II conjugating genes is altered in a species-distinct manner on treatment with PPARalpha activators. As a result of such regulatory processes, PPARalpha affects the homeostasis of both its own natural ligands and other compounds including bile acids. At the non-genomic level, PPARalpha activators can act as competitive inhibitors for inactivating other molecules, leading to drug-drug interactions. These global effects of PPARalpha activators on the activity of XMEs are of physiological and pharmaceutical importance, and demonstrate that thorough studies of the actions on XMEs of each novel PPARalpha agonist are warranted.

Tailor-made pharmacotherapy: future developments and ethical challenges in the field of pharmacogenomics

Pharmacogenomics is the study of the myriad interactions between genes and pharmacotherapy. Developments in pharmacogenomics have changed and will affect pharmaceutical research, drug development and the practice of medicine in a significant way. In this article, we make an inventory of the ethical implications that might arise as a result of possible developments in pharmacogenomics and investigate whether the present ethical framework will be able to adequately answer arising questions. We think that many of the questions related to the consequences of pharmacogenomics are answerable along the lines of present ethical thinking. We also believe, however, that many 'changes of degree' may result in a 'change of kind.' We therefore think that pharmacogenomics may potentially have such a profound influence on scientific research and the pharmaceutical industry, the practice of medicine and society at large, that this will generate its own unique dynamic, which will require new ethical research. We suggest that the notion of 'responsibility' will be a major focus of such research.

Automated protein structure homology modeling: a progress report

Understanding the molecular function of proteins is greatly enhanced by insights gained from their three-dimensional structures. Since experimental structures are only available for a small fraction of proteins, computational methods for protein structure modeling play an increasingly important role. Comparative protein structure modeling is currently the most accurate method, yielding models suitable for a wide spectrum of applications, such as structure-guided drug development or virtual screening. Stable and reliable automated prediction pipelines have been developed to apply large-scale comparative modeling to whole genomes or entire sequence databases. Model repositories give access to these annotated and evaluated models. In this review, we will discuss recent developments in automated comparative modeling and provide selected examples illustrating the use of homology models.

Genomics and proteomics tools for compound mode-of-action studies in drug discovery

A broad range of genomics and proteomics technologies are increasingly being integrated into emerging research fields such as pharmacogenomics, pharmacoproteomics, chemogenomics, chemical genetics, and chemical biology. Here we review applications of genomic and proteomic technologies to drug mechanism-of-action studies and how these are beginning to impact the drug discovery process.

Basic mechanisms of cardiac impulse propagation and associated arrhythmias

Propagation of excitation in the heart involves action potential (AP) generation by cardiac cells and its propagation in the multicellular tissue. AP conduction is the outcome of complex interactions between cellular electrical activity, electrical cell-to-cell communication, and the cardiac tissue structure. As shown in this review, strong interactions occur among these determinants of electrical impulse propagation. A special form of conduction that underlies many cardiac arrhythmias involves circulating excitation. In this situation, the curvature of the propagating excitation wavefront and the interaction of the wavefront with the repolarization tail of the preceding wave are additional important determinants of impulse propagation. This review attempts to synthesize results from computer simulations and experimental preparations to define mechanisms and biophysical principles that govern normal and abnormal conduction in the heart.

Genetic polymorphisms, drugs, and proarrhythmia

Humans vary widely in their response to drug therapy. This may reflect variability in the relationship between a drug dose and the concentrations of drug and metabolite(s) at relevant target sites; this is termed pharmacokinetic variability. Another mechanism is that individuals vary in their response to identical exposures to drug (pharmacodynamic variability). In this case, there may be variability in the target molecule(s) with which a drug interacts, or more generally in the broad biologic context in which the drug-target interaction occurs; for example, ischemia, electrolyte disturbances, or hypertrophy can all modulate drug effects. Variants in the genes encoding proteins important for pharmacokinetics or for pharmacodynamics have now been described as important contributors to variable drug actions, including proarrhythmia, and are described here. These increasingly well-recognized examples have two important implications; first, it may be possible to develop drugs devoid of heretofore-unexplained adverse effects and, second, it may become possible to preselect drug for individual patients based on specific genetic factors.