Cardiovascular pharmacogenomics: current status, future prospects

A Randomized and Clinical Effectiveness Trial Comparing Two Pharmacogenetic Algorithms and Standard Care for Individualizing Warfarin Dosing (CoumaGen-II)

Background—

Warfarin is characterized by marked variations in individual dose requirements and a narrow therapeutic window. Pharmacogenetics (PG) could improve dosing efficiency and safety, but clinical trials evidence is meager.

Methods and Results—

A Randomized and Clinical Effectiveness Trial Comparing Two Pharmacogenetic Algorithms and Standard Care for Individualizing Warfarin Dosing (CoumaGen-II) comprised 2 comparisons: (1) a blinded, randomized comparison of a modified 1-step (PG-1) with a 3-step algorithm (PG-2) (N=504), and (2) a clinical effectiveness comparison of PG guidance with use of either algorithm with standard dosing in a parallel control group (N=1866). A rapid method provided same-day CYP2C9 and VKORC1 genotyping. Primary outcomes were percentage of out-of-range international normalized ratios at 1 and 3 months and percentage of time in therapeutic range. Primary analysis was modified intention to treat. In the randomized comparison, PG-2 was noninferior but not superior to PG-1 for percentage of out-of-range international normalized ratios at 1 month and 3 months and for percentage of time in therapeutic range at 3 months. However, the combined PG cohort was superior to the parallel controls (percentage of out-of-range international normalized ratios 31% versus 42% at 1 month; 30% versus 42% at 3 months; percentage of time in therapeutic range 69% versus 58%, 71% versus 59%, respectively, all P <0.001). Differences persisted after adjustment for age, sex, and clinical indication. There were fewer percentage international normalized ratios ≥4 and ≤1.5 and serious adverse events at 3 months (4.5% versus 9.4% of patients, P <0.001) with PG guidance.

Conclusions—

These findings suggest that PG dosing should be considered for broader clinical application, a proposal that is being tested further in 3 major randomized trials. The simpler 1-step PG algorithm provided equivalent results and may be preferable for clinical application.

Clinical Trial Registration—

URL: http://www.clinicaltrials.gov . Unique identifier: NCT00927862.

Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver

Liver cytochrome P450s (P450s) play critical roles in drug metabolism, toxicology, and metabolic processes. Despite rapid progress in the understanding of these enzymes, a systematic investigation of the full spectrum of functionality of individual P450s, the interrelationship or networks connecting them, and the genetic control of each gene/enzyme is lacking. To this end, we genotyped, expression-profiled, and measured P450 activities of 466 human liver samples and applied a systems biology approach via the integration of genetics, gene expression, and enzyme activity measurements. We found that most P450s were positively correlated among themselves and were highly correlated with known regulators as well as thousands of other genes enriched for pathways relevant to the metabolism of drugs, fatty acids, amino acids, and steroids. Genome-wide association analyses between genetic polymorphisms and P450 expression or enzyme activities revealed sets of SNPs associated with P450 traits, and suggested the existence of both cis-regulation of P450 expression (especially for CYP2D6) and more complex trans-regulation of P450 activity. Several novel SNPs associated with CYP2D6 expression and enzyme activity were validated in an independent human cohort. By constructing a weighted coexpression network and a Bayesian regulatory network, we defined the human liver transcriptional network structure, uncovered subnetworks representative of the P450 regulatory system, and identified novel candidate regulatory genes, namely, EHHADH, SLC10A1, and AKR1D1. The P450 subnetworks were then validated using gene signatures responsive to ligands of known P450 regulators in mouse and rat. This systematic survey provides a comprehensive view of the functionality, genetic control, and interactions of P450s.

Inconsistencies in the genetic prediction of HDL cholesterol versus atherosclerosis

PURPOSE OF REVIEW

High-density lipoprotein (HDL) is generally perceived as having a protective role with respect to cardiovascular disease. The metabolism of HDL is mediated through a complex network of apoproteins, enzymes and transfer proteins. Genetic variants within this network can increase plasma HDL, but not with uniformly beneficial clinical outcomes. The purpose of this review is to explore and propose mechanisms for these discrepant observations.

RECENT FINDINGS

Recent developments in this area include new observations of genetic variants that paradoxically increase both HDL and cardiovascular risk. Also discussed are newly observed, function-altering modifications of the HDL particle. Proposed explanations include the segregation of the genetic variants associated with the respective endpoints of plasma HDL and cardiovascular risk. Functionally impaired but quantitatively robust plasma HDL and the emerging understanding of proinflammatory HDL also may contribute to our understanding of discordant observations.

SUMMARY

Enhanced understanding of these relationships may allow a more accurate assessment of clinical risk based on plasma HDL and help explain why HDL may, in some circumstances, be an inappropriate therapeutic target.

Randomized Trial of Genotype-Guided Versus Standard Warfarin Dosing in Patients Initiating Oral Anticoagulation

Background— Pharmacogenetic-guided dosing of warfarin is a promising application of “personalized medicine” but has not been adequately tested in randomized trials.

Methods and Results— Consenting patients (n=206) being initiated on warfarin were randomized to pharmacogenetic-guided or standard dosing. Buccal swab DNA was genotyped for CYP2C9 *2 and CYP2C9 * 3 and VKORC1 C1173T with a rapid assay. Standard dosing followed an empirical protocol, whereas pharmacogenetic-guided dosing followed a regression equation including the 3 genetic variants and age, sex, and weight. Prothrombin time international normalized ratio (INR) was measured routinely on days 0, 3, 5, 8, 21, 60, and 90. A research pharmacist unblinded to treatment strategy managed dose adjustments. Patients were followed up for up to 3 months. Pharmacogenetic-guided predicted doses more accurately approximated stable doses ( P <0.001), resulting in smaller ( P =0.002) and fewer ( P =0.03) dosing changes and INRs ( P =0.06). However, percent out-of-range INRs (pharmacogenetic=30.7%, standard=33.1%), the primary end point, did not differ significantly between arms. Despite this, when restricted to wild-type patients (who required larger doses; P =0.001) and multiple variant carriers (who required smaller doses; P <0.001) in exploratory analyses, results (pharmacogenetic=29%, standard=39%) achieved nominal significance ( P =0.03). Multiple variant allele carriers were at increased risk of an INR of ≥4 ( P =0.03).

Conclusions— An algorithm guided by pharmacogenetic and clinical factors improved the accuracy and efficiency of warfarin dose initiation. Despite this, the primary end point of a reduction in out-of-range INRs was not achieved. In subset analyses, pharmacogenetic guidance showed promise for wild-type and multiple variant genotypes.

Associations with myocardial infarction of six polymorphisms selected from a three-stage genome-wide association study

BACKGROUND

Coronary heart disease, including its clinical manifestation, myocardial infarction (MI), is a common, complex disease with a substantive genetic component. State-of-the-art genetic epidemiology evaluates thousands of single nucleotide polymorphisms (SNPs) in association with disease cases and controls. In an independent but demographically similar population, this study tested 6 SNPs that were previously reported to be associated with MI.

METHODS

Patients hospitalized for an acute MI (n = 413) at an early age (men < 55 years, women < 65 years) were compared with age-discordant (men > or = 65 years, women > or = 70 years) control patients (n = 792) who had no MI history and no hospitalization for MI at index angiography or during longitudinal follow-up. Six SNPs were genotyped in the genes palladin, ROS1, TAS2R50, OR13G1, and ZNF627.

RESULTS

Findings were not different from the null hypothesis, with ZNF627 (AG vs. GG: odds ratio [OR] 1.47, P = .16; AA vs. GG: OR 1.20, P = .50) and both ROS1 SNPs (GG vs AA: OR 0.72, P = .21; CC vs GG: OR 0.74, P = .24) showing potentially interesting ORs but nonsignificant probabilities. After full adjustment for all SNPs and covariables, only the ZNF627 heterozygote genotype had OR > 1.5 (P = .14). Comparison of MI cases with controls without obstructive coronary artery disease and analyses stratified by sex provided similar findings.

CONCLUSIONS

Six SNPs previously reported to be associated with MI were not validated, suggesting that further investigation is needed to verify the applicability of those SNPs to cardiovascular medicine. These findings emphasize the high potential for false-positive results even in staged genome-wide association studies and further emphasize the need for continued refinement of cardiovascular genetic methodologies for clinical application.

Rapid melting curve analysis for genetic variants that underlie inter-individual variability in stable warfarin dosing

Warfarin anticoagulation therapy is complicated by its narrow therapeutic index and by wide inter-individual differences in dosing requirements arising, in part, from genetic factors. The present report describes the development, validation and feasibility testing of a rapid genotyping assay that concurrently detects the CYP2C9*2 and *3 variants along with the VKORC1 C1173T polymorphism. The study employed melting curve analysis using labeled probes and compared two detection instruments (the HR-1 and the R.A.P.I.D. LT) to two previously validated methods, 5' nuclease allelic discrimination (Taqman) assay and cycle sequencing. The HR-1 detected 189 true negatives and 113 true positives; 1 wild-type sample was mistyped as a heterozygote by both instruments. Sequencing of that sample confirmed it to be a CC homozygote; however, a rare C > T polymorphism was discovered 1 base 5' from the *2 polymorphic site, presumably causing the mistaken genotype by melting curve. Both methods had sensitivity = 1.00 and specificity > 0.99. Combined with a method for rapid buccal swab DNA extraction, genotyping results were obtained in a median of 59 min. These methods should facilitate genotype-driven warfarin dosing in "real-time" clinical practice.

Multiple less common genetic variants explain the association of the cholesteryl ester transfer protein gene with coronary artery disease

OBJECTIVES

The objective of this study was to identify associations of the cholesteryl ester transfer protein (CETP) gene with coronary artery disease (CAD) with tagging (t) single nucleotide polymorphisms (SNPs) chosen to optimally account for intra-genic variation.

BACKGROUND

The CETP gene plays a critical role in lipoprotein metabolism, but the common and well-studied TaqIB variant is inconsistently predictive of CAD.

METHODS

From a deoxyribonucleic acid bank of 10,020 individuals, nondiabetic nonsmoking patients (n = 4,811) with angiographically defined, clinically significant CAD (> or =70% stenosis) or normal coronaries were genotyped for 11 CETP tSNPs. Myocardial infarction (MI) and lipid levels were evaluated as secondary end points.

RESULTS

Analysis of single tSNPs, corrected for multiple comparisons (p < 0.00485), identified allele +1086A to be associated with CAD (p = 0.0034). Suggestive allelic and significant genotypic associations were found for -631AA (odds ratio [OR] = 3.95, p = 0.004 vs. CC) and +2389GA (OR = 1.21, p = 0.003 vs. GG). Haplotype analysis by linkage disequilibrium (LD) group revealed a CAD association for LD group B (p = 0.0025 across T+1086A, C+878T, C+408T) and near significance for LD group A (p = 0.013 across C-631A, MspI, G+2389A). A weak protective trend for TaqIB was eliminated by adjustment for other tSNPs, and haplotype analyses suggested that TaqIB was simply a marker for other tSNPs or haplotypes. No tSNP or haplotype associations with MI were found.

CONCLUSIONS

Multiple, less common SNPs and haplotype variants underlie CETP-related CAD risk, for which the common TaqIB variant is simply a poor marker. The occurrence of risk-related variants on separate haplotypes suggests genetic-risk complexity and allelic heterogeneity. (Database Registry of the Intermountain Heart Collaborative Study; http://clinicaltrials.gov/ct/show/NCT00406185?order=1; NCT00406185).

beta2 adrenoceptor (ADRB2) pharmacogenetics and cardiovascular phenotypes during laryngoscopy and tracheal intubation

Pharmacogenetics is the study of genetic variations that cause a variable drug response characterized by alteration in drug metabolism or in pharmacodynamics. The polymorphisms in genes encoding receptors relevant to treatment cause variation in sensitivity to many drugs. beta2 Adrenoceptor genetic variation contributes to regulation of blood pressure and hemodynamic changes by mediating peripheral vasodilatation. Laryngoscopy and tracheal intubation associated with hemodynamic changes. Although there are four nonsynomic single-nucleotide polymorphisms (SNPs) of beta2 adrenoceptor gene, codon 16 (Arg16Gly) and codon 27 (Gln27Glu) SNPs are both common and functionally important. In this paper, the authors investigated the beta2 adrenoceptor Gly16 and Glu27 SNPs in response to drugs relevant to anesthesia and how these SNPs impacted upon the cardiovascular phenotypes. The authors measured arterial systolic and diastolic blood pressure, heart rate, and rate-pressure product before induction of anesthesia and 1 min following laryngoscopy and tracheal intubation. Genomic DNA was amplified and genotyped using allele-specific polymerase chain reaction (ASPCR) and restriction fragment length polymorphism (RFLP) assays, respectively. When the authors compared hemodynamic results according to genotypes, the patients with Gln homozygote allele at codon 27 exhibited significant increase of heart rate than patients with Glu allele after laryngoscope and tracheal intubation.

Clinical Translation of Genotyping and Haplotyping Data

The completion of the Human Genome Project has raised expectations for the translation of genomic knowledge into clinical forms that would lead to improved diagnosis of diseases and identification of new drug targets. Such an opportunity is quite challenging within science and society, although there is still uncertainty regarding its outcomes in new drug development and healthcare. Undoubtedly, however, the recent approval by the US FDA of the first two pharmacogenomic tests for genotyping drug-metabolising enzymes is expected to empower and eventually lead to general applicability of various genetic diagnostic tools to improve pharmacotherapy outcomes in the post-genomic era. To this end, the application of genomic knowledge and technologies in everyday clinical practice leads personalised medicine concepts towards the achievement of individualised drug selection and dosage profiling (i.e. pharmacotyping) for ensuring maximum drug effectiveness and safety. Within this framework, pharmacogenomic information can implement the existing clinical pharmacology experience in clinical diagnosis and drug delivery. The latter can be further advanced through the development of workflow information-based operating systems in healthcare to support the utilisation, assessment and outcome of engaged clinical and genomic information. Such a direction may help to suitably revise and adjust clinical regulatory guidelines as well as clinical pharmacology guidelines. This will further facilitate better designing of clinical trials for new drug development as well as pharmacovigilance registries and evaluation of these data. To critically describe the existing environment, this article comprehensively discusses scientific efforts aimed at making clinical translation of genotyping and haplotyping data more efficient and productive in forms that are readily applicable in everyday healthcare. In addition, specific and systematic pharmacogenomic and clinical attempts related to the development of new molecularly targeted drugs, as well as improvement of the efficacy and safety of commonly prescribed drugs, are presented. To this end, the clinical pharmacogenomic experience gained thus far in the use of tyrosine kinase inhibitors in oncology, as well as the process of empowerment through the use of genomic knowledge of the cardiac safety of drugs modulating the function of the human ether-à-go-go-related gene (HERG) potassium channel, represent examples of how the implementation of clinical experience with genomic information guides the development of new drugs and the improvement of pharmacotherapy outcomes.

Pharmacogenomics in cardiovascular disease: the role of single nucleotide polymorphisms in improving drug therapy

Pharmacogenomics is the study of how an individual's genetic inheritance affects the body's response to drugs. Pharmacogenomics holds the promise that drugs might one day be tailor-made for individuals and adapted to an individual's genetic makeup. Several studies have shown that both adverse and beneficial responses to cardiovascular drugs can be influenced by single nucleotide polymorphisms in genes coding for metabolising enzymes, drug transporters and drug targets. Despite the large amount of data about gene-drug interactions, the translation of pharmacogenomics in clinical practise is slow. To improve this, there is a need of new technology and large prospective trials allowing for simultaneous analysis of multiple genetic variants in molecular pathways that could affect drug disposition and action.

Improving pharmacotherapy outcomes by pharmacogenomics: from expectation to reality?

The genomic era is now a reality and the extraction of genomic information with a practical value in healthcare represents the next challenge following the completion of the Human Genome Project. To this end, the first pharmacogenomics test approved by the US Food & Drug Administration for assessing cytochrome P450 (CYP)2D6 and CYP2C19 genotype in the implementation of pharmacotherapy decisions in patients, is expected to improve pharmaceutical care outcomes, at least for drugs that are substrates or inhibitors of these enzymes. Furthermore, the progress already achieved and the experience gained in the fields of pharmacogenomics and personalized medicine has clearly demonstrated that an interdisciplinary approach could better serve the target of improving pharmacotherapy outcomes in routine clinical practice. Such an approach will obviously move drug prescription towards pharmacotyping, a stage where the drug selection and dosage process carried out by medical practitioners for any given patient will be advanced by genomic knowledge and information.

Toll-like receptor 4 gene Asp299Gly polymorphism is associated with reductions in vascular inflammation, angiographic coronary artery disease, and clinical diabetes

BACKGROUND

Coronary artery disease (CAD) and, increasingly, diabetes are recognized as having an inflammatory basis. Membrane toll-like receptors (TLRs) activate signaling pathways that up-regulate inflammation. We evaluated whether the Asp299Gly polymorphism in the TLR4 gene, which impairs inflammatory responses, is associated with reduced vascular inflammation (assessed by C-reactive protein [CRP]) and a decreased risk for CAD and diabetes.

METHODS

1894 patients without acute myocardial infarction undergoing coronary angiography were studied. Genotyping was performed by real-time polymerase chain reaction. CAD was defined as >or=70% stenosis. Diabetes was diagnosed by patients' referring physicians. CRP was measured by fluorescence polarization immunoassay. Regression analyses adjusted for traditional cardiac risk factors.

RESULTS

Patients averaged 64 +/- 11 years of age, and 69% were male. Asp299Gly genotype frequencies were: AA = 0.911 (n = 1725), AG = 0.086 (n = 164), and GG = 0.003 (n = 5), in keeping with Hardy-Weinberg equilibrium. CRP was lower among G-allele carriers (median = 1.11 mg/dL) than wild-type (AA) subjects (1.23 mg/dL, adjusted P = .044). G-allele carriers also had a lower prevalence of CAD (65% vs. 73%, OR = 0.67, CI = 0.46-0.99, adjusted P = .048) and diabetes (11% vs. 18%, OR = 0.63, CI = 0.42-0.95, adjusted P = .029), which persisted in multivariate logistic regression analyses. 299Gly carriage did not affect clinical outcomes nor interact with statin therapy.

CONCLUSIONS

The TLR4 299Gly allele was associated with reduced CRP levels and, in parallel, a decreased risk of angiographic CAD and clinical diabetes. These findings suggest that down-regulation of innate immune responsiveness could beneficially modify CAD and diabetes risk and might provide a novel basis for genetic risk stratification and therapeutic targeting.

Genetic variation and exposure related risk estimation: will toxicology enter a new era? DNA repair and cancer as a paradigm

With the vast technological and informational resources increasingly available from investments in "genomics," toxicology and much of biological science, is faced with previously undreamed of opportunities and equally daunting challenges. The ability to generate the large quantities of data becoming routinely available could not be imagined a decade ago. The complexities of data analysis are increasingly the rate-limiting element in scientific advances. The expectations that these large scientific investments will reduce the incidence of human disease and improve health are very high. An emphasis on genetic variation and Toxicogenetics is expected to yield risk estimates for specific rather than average individuals and individuals with varied lifestyles and complex patterns of exposure. Examples from studies of polymorphic variation in DNA repair genes in the healthy population and cancer risk highlight the complexity and challenges of incorporating genetic variation into quantitative estimates of risk associated with environmentally relevant exposures. Similar issues exist in selecting the animal models most appropriate for predicting human risk from environmental exposures to toxic agents.

Pharmacogenomics and drug response in cardiovascular disorders

There are a total of 17 families of drugs that are used for treating the heterogeneous group of cardiovascular diseases. We propose a comprehensive pharmacogenomic approach in the field of cardiovascular therapy that considers the five following sources of variability: the genetics of pharmacokinetics, the genetics of pharmacodynamics (drug targets), genetics linked to a defined pathology and its corresponding drug therapies, the genetics of physiologic regulation, and environmental–genetic interactions. Examples of the genetics of pharmacokinetics are presented for phase I (cytochromes P450) and phase II (conjugating enzymes) drug-metabolizing enzymes and for phase III drug transporters. The example used to explain the genetics of pharmacodynamics is glycoprotein IIIa and the response to antiplatelet effects of aspirin. Genetics linked to a defined pathology and its corresponding drug therapies is exemplified by ADRB1, ACE, CETP and APOE and drug response in metabolic syndrome. The examples of cytochrome P450s, APOE and ADRB2 in relation to ethnicity, age and gender are presented to describe genetics of physiologic regulation. Finally, environmental–genetic interactions are exemplified by CYP7A1 and the effects of diet on plasma lipid levels, and by APOE and the effects of smoking in cardiovascular disease. We illustrate this five-tiered approach using examples of cardiovascular drugs in relation to genetic polymorphism.

From pharmacogenetics to personalized medicine: a vital need for educating health professionals and the community

The field of pharmacogenetics will soon celebrate its 50th anniversary. Although science has delivered an impressive amount of information in these 50 years, pharmacogenetics has suffered from lack of integration into clinical practice. There are several reasons for this, including the unmet need for education at medical schools and the lack of awareness about the impact of genetic medicine on healthcare in the community. Recently, the FDA announced that it considers pharmacogenomics one of three major opportunities on the critical path to new medical products. This notion by the FDA is filling the regulatory void that existed between drug developers and drug users. However, in order to bring pharmacogenetic testing to the prescription pad successfully, healthcare professionals and policy makers, as well as patients, need to have the necessary background knowledge for making educated treatment decisions. To effectively move pharmacogenetics into everyday medicine, it is therefore imperative for scientists and teachers in the field to take on the challenge of disseminating pharmacogenetic insights to a broader audience.