Pharmacogenetics

Background

Pharmacogenetics describes how genes influence drug response. Genes can impact either the pharmacokinetics or pharmacodynamics of a drug to influence the dose required and associated therapeutic or toxic effects. Pharmacogenetic testing performed before drug administration may guide the selection of drugs and drug dosing. Post-therapeutic pharmacogenetic testing can explain an adverse drug reaction, including therapeutic failure.

Content

This chapter reviews pharmacokinetics and pharmacodynamics, the two major processes involved in drug response, and describes how genes that encode for proteins involved in these processes influence drug response. Important nongenetic factors that influence drug response, such as drug formulation differences, drug–drug and food–drug interactions, and clinical status are discussed, along with appropriate specimens and analytical strategies for performing, reporting, and interpreting pharmacogenetic testing results. In addition, specific gene–drug examples are described in detail relative to the nomenclature of genetic variants and allele assignments, genotype-phenotype predictions, clinical applications, and associated guidance for dosing.

Drug response

For simplicity, the term drug is used throughout this chapter to reflect any xenobiotic (foreign compound absorbed by the human body) that is capable of evoking a physiologic or behavioral response. Response to drugs depends on many variables, such as drug formulation, route of administration, age, gender, clinical status (e.g., kidney function, liver function, protein status), comedications, and genetics. Most drugs are selected and initially dosed according to drug labeling, clinical experience, and institutional protocols that stem from population-based dosage and dose frequency recommendations. Many of the nongenetic variables affecting drug response are measurable and are currently applied to drug therapy decisions, but dose optimization remains largely dependent on trial and error. Minimizing this process of trial and error with pharmacogenetics is proposed to improve the efficacy of drugs and prevent up to 60% of adverse drug reactions. ^,

Pharmacogenetic testing is designed to predict specific aspects of the two major processes upon which drug response is based: pharmacokinetics and pharmacodynamics. Pharmacokinetics describes how the body acts on a drug, often called “ADME,” referring to absorption, distribution, metabolism, and elimination. Genes that encode drug metabolizing enzymes and transport proteins are involved in pharmacokinetics. Pharmacodynamics describes how the body responds to drugs, both desirable (e.g., therapeutic) and undesirable (e.g., therapeutic failure and/or toxicity). Genes that encode for mechanistic proteins such as enzymes, receptors, and ion channels are involved in pharmacodynamics. Sometimes drugs cause adverse effects due to mechanisms that are unrelated to the intended use of the drug. For example, carbamazepine, a drug used to treat seizures and neuropathic pain largely by inhibiting voltage gated sodium channels, can stimulate the immune system, leading to a severe cutaneous adverse reaction that can be life-threatening. ^, This adverse reaction is attributed to the presence of the HLA-B*15:02 allele, representing variation in the genes that code for the human leukocyte antigen (HLA) system, and is unrelated to the mechanisms responsible for managing seizures and pain. The adverse reaction is also unrelated to the pharmacokinetics of carbamazepine. Pretherapeutic testing to detect this allele in people being considered for carbamazepine therapy is recommended for vulnerable populations. ^,

There are often many genes associated with the pharmacokinetics and pharmacodynamics of a drug. Selecting drugs and drug dosing for an individual should consider the clinically significant genes involved in pharmacokinetics and pharmacodynamics, in combination with relevant nongenetic factors. After drug and dose are selected, response to the drug should be monitored. If the response is desirable (therapeutic), the pharmacokinetics and pharmacodynamics are appropriate. Therapeutic failure may occur if the concentrations of active drug are insufficient (e.g., pharmacokinetic variability) or if the physiology to elicit the response to the drug is absent or impaired (e.g., pharmacodynamic variability). If the response is not optimal or is undesirable, therapy may need to be adjusted. Dose of a drug is adjusted based on results of clinical measurements (e.g., blood pressure for antihypertensive drugs), therapeutic drug monitoring (e.g., voriconazole concentrations in the blood), or monitoring biochemical markers of response (e.g., creatine kinase for statin surveillance). Other examples are presented below.

The goal of therapeutic drug monitoring is to adjust the dose to achieve blood concentrations of active drug that fall within an established therapeutic range at particular times after dose administration. This practice of dose adjustment is common to immunosuppressants such as tacrolimus. Thus blood samples are collected at specific times after administration of tacrolimus, ideally after the drug concentrations have achieved steady state. The dose is adjusted to achieve concentrations that consistently fall within the therapeutic range selected for the patient population and clinical indication, noting that pharmacokinetic variation can contribute to differences in time to achieve a steady-state drug concentration. Pretherapeutic pharmacogenetic testing can guide the initial dose of tacrolimus and predict an altered time to steady state.

An example of a biochemical marker of response is the international normalized ratio (INR) that is calculated from prothrombin time (PT) ( Box 73.1 ) and is used to guide and adjust doses of the common anticoagulant drug warfarin. As with tacrolimus, blood samples are collected at specific times after administration of warfarin. The dose is adjusted until the INR consistently falls within a target range that is selected for the patient population and clinical indication. The target INR range is set to 2.0 to 3.0 for most indications. Genetic testing can help predict a therapeutic dose, thus making warfarin a drug of pharmacogenetic interest.

Adverse drug reactions (therapeutic failure or toxicity) that are dose-dependent are classified as “type A” reactions. Such scenarios can be managed by adjusting the dose of a drug based on clinical or laboratory monitoring of drug concentrations and/or biomarkers. Inappropriate dosing of tacrolimus or warfarin can lead to type A adverse reactions. Adverse drug reactions may also occur independently of dose and are classified as “type B” reactions. As such, monitoring and adjusting dose will be unsuccessful. In this case, an alternate drug is required. The carbamazepine-induced hypersensitivity example illustrates a type B reaction. Pretherapeutic pharmacogenetic testing may predict vulnerability to type A and type B adverse reactions if these drugs are administered.

Likelihood of a desirable (therapeutic) response can be predicted through pharmacogenetics as well. The US Food and Drug Administration (FDA) designates in vitro diagnostic (IVD) devices that identify candidates for a specific therapeutic product as companion diagnostic devices. The labeling for both the IVD diagnostic and the companion therapeutic product stipulate the pretherapeutic use of the test to determine whether a person is likely to respond to the therapeutic product. ^, Nearly all currently approved companion diagnostics are for use in treating cancer and are designed to detect drug targets (pharmacodynamics), be they proteins or somatic gene mutations, in tumor tissue. Presence of the drug target qualifies a patient to receive the corresponding companion drug. Absence of the drug target suggests that a patient should not receive the companion drug and should be considered for an alternate therapy. Examples of approved companion diagnostics for cancer treatment are shown in Table 73.1 . These tests have demonstrated clinical validity and have improved patient outcomes for select drugs, such as for prescribing cetuximab in colorectal carcinoma based on KRAS mutation results. This approach to personalized care is also prominent in drug development efforts and clinical trials for new drugs and new drug indications.

Pharmacokinetics

The first recognized pharmacogenetic findings described pharmacokinetic variation, specifically interindividual differences in drug metabolism. The early focus on drug metabolism reflects the fact that measurements of drug and drug metabolite concentrations in biological fluids predate detailed understanding of genetics and development of most biomarkers that describe pharmacodynamics. Distinct metabolic phenotypes were characterized with biological fluid testing and patterns of results were subsequently found to cluster within families. For example, the metabolic phenotype for N -acetyltransferase (NAT) and isoniazid, a drug used to treat tuberculosis, was recognized in the 1950s. ^, Population studies revealed a bimodal distribution in plasma and urine concentrations of the N -acetylated isoniazid metabolite, that correlated with the phenotype. An example of the phenotypic differences observed with metabolic ratios in urine is shown in Fig. 73.1 . The concentration of the parent drug was also correlated with the prevalence of toxic symptoms, including hepatotoxicity and a painful, progressive peripheral neuropathy that affected up to one-third of white and African American patients. Such testing defines the phenotypic “state” rather than the genetic “trait” and can require collection of several biological specimens, which can be costly. Phenotype testing may look at protein function as well, such as direct testing of enzyme activity. Phenotype testing is not routinely performed when informative gene-based testing is available.

When thinking about the role of drug metabolism and associated genes in pharmacogenetics, one must consider whether the drug administered is active or inactive. Parent drugs are administered as either active drug or as inactive prodrugs . A prodrug is a compound that requires metabolism to be converted to an active drug. Many of the drugs discussed in this chapter are classified as a prodrug or active drug in Table 73.2 . Both prodrugs and active drugs are usually metabolized by many enzymes, producing both active and inactive metabolites. Fig. 73.2 illustrates the common metabolic relationship for prodrugs, active drugs, and metabolites (active and/or inactive). Primary active metabolites are identified for the specific drug examples shown in Table 73.2 .

Metabolic phenotypes, whether determined directly or predicted by genotype, typically include normal (formerly extensive), intermediate, and poor metabolizers. For some enzymes, rapid and ultra-rapid metabolizer phenotypes are also described. The normal metabolizer is consistent with typical metabolic function and expression for the reference enzymes evaluated. Genetic variants can affect the function or expression of the enzymes and, consequently, the predicted phenotype. Two copies of no function (loss-of-function) alleles predicts the poor metabolizer phenotype. For patients who are poor metabolizers , consideration should be given to the use of therapeutic products that do not require the specific drug metabolizing enzymes coded by the affected gene. A dose-adjustment could also be considered. The intermediate metabolizer phenotype predicts reduced metabolic activity as compared to the normal metabolizer phenotype. The rapid and ultrarapid metabolizer phenotypes predict increased activity or expression and often reflects more than two copies of a functional gene (e.g., gene duplication events).

Multiple drug metabolizing enzymes may be involved in activation and/or inactivation of a drug. The composite drug metabolizer phenotype must consider the impact of all known metabolic pathways. The phenotype may also be affected by nongenetic factors such as drug–drug interactions. Depending on the scenario, the dose of a drug may be adjusted to compensate for the predicted phenotype. Therefore clinical use of pharmacogenetic testing can guide both drug and dose selection by understanding how the genetic variation affects pharmacokinetics.

Drug transporter proteins may also affect pharmacokinetics of a drug by preventing or enhancing the transport of drug molecules across membranes. Drug transporter proteins may affect absorption, distribution, and/or elimination of a drug. A loss-of-function variant in a gene that codes for a drug transporter protein may prevent drug absorption, leading to therapeutic failure, or it may prevent elimination of a drug, leading to drug accumulation that can contribute to a type A adverse reaction. Variant drug transporters may also prevent or enhance compartmental distributions, such as transport of drug into and out of the brain. The composite roles of both drug transporter proteins and drug metabolizing enzymes will affect overall pharmacokinetics of a drug and the associated phenotype for a person.

An example pharmacokinetic pathway for the analgesic opioid drug codeine is shown in Fig. 73.3 . Codeine is a prodrug, and the active drug is morphine. Bioactivation of codeine occurs primarily through the drug metabolizing enzyme cytochrome P450 2D6 (CYP2D6). Codeine is also inactivated by reactions mediated by cytochrome P450 3A4 (CYP3A4) and uridine diphosphate glucuronic acid glucuronosyltransferase 2B7 (UGT2B7). The UGT family of drug metabolizing enzymes mediates the transferase reaction necessary to form glucuronide metabolites that are in general more water-soluble than the non-glucuronidated forms, which promotes drug elimination. Morphine is inactivated by reactions mediated by several UGT enzymes. The various glucuronide metabolites are transported out of the liver cell for elimination by drug transporters, including ABCB1, ABCC2, ABCC3, and SLCO1B1. This example demonstrates that several drug metabolizing enzymes and drug transporters may be involved in the distribution, metabolism, and elimination of a drug.

Pharmacodynamics

Pharmacogenetics of pharmacodynamics can predict desirable and undesirable responses to a drug. The range of types of pharmacodynamic targets is vast, and includes receptors, ion channels, other signaling proteins, enzymes, and the immune system. Pharmacodynamic responses can be elicited by any active component of a drug, including active metabolites. The overall response phenotype represents a composite of how all pharmacodynamic and pharmacokinetic processes function, representing both genetic and nongenetic factors. Achieving appropriate concentrations of active drug and/or metabolites (pharmacokinetics) does not ensure but may increase the likelihood that a person will respond to the drug.

An example pharmacodynamic pathway for the anticoagulant drug warfarin is illustrated in Fig. 73.4 . As shown, warfarin is a racemic mixture of R- and S-stereoisomers. The primary pharmacodynamic target of warfarin is vitamin K epoxide reductase complex subunit 1 (VKOR). Other proteins involved in the pharmacodynamics of warfarin include epoxide hydrolase 1 (EPHX1), cytochrome P450 4F2 (CYP4F2), gamma-glutamyl carboxylase (GGXC), calumenin (CALU), and the various blood clotting factors that are activated by vitamin K. ^, Variants in the VKOR gene, VKORC1, are well recognized to affect the sensitivity to warfarin, which is discussed in detail later in this chapter.

Implementation of pharmacogenetics

Pharmacogenetic testing is intended to predict and/or explain discrete aspects of pharmacokinetics and pharmacodynamics to guide drug and dose selection. Once a drug is initiated, the response is monitored and dosing optimized with clinical and/or laboratory tools. It is not practical, medically indicated, or cost-effective to apply pharmacogenetics to every drug therapy situation. The pharmacogenetic tests that have proven most successful are the ones that produce actionable results. Many resources for labeling information, gene–drug associations, and clinical consensus guidelines are maintained and updated electronically. In general, these guidelines promote implementation of pharmacogenetic testing when patient outcome can be improved with specific dosing strategies or alternative therapeutic choices. Some specific gene–drug relationships for which the FDA labeling includes pharmacogenetic information are shown in Table 73.3 . These gene–drug examples apply to medical disciplines that include oncology, psychiatry, neurology, infectious disease, pain management, and cardiology. The FDA continues to gauge the evidence for clinical relevance of additional gene-drug associations and maintains a very informative Table of Pharmacogenetic Associations. Most areas of medicine can benefit from pharmacogenetic testing, and the number of clinically useful targets will only increase as comprehensive pharmacogenetic testing becomes more widely available.

Logistics of pharmacogenetics in a clinical setting

Analytical strategies

The analytical strategy used in pharmacogenetic testing depends on a variety of factors, such as the complexity of the gene; the extent, frequency, and type of genetic variation; and the time needed for return of the results. Most genotyping assays cannot detect all variants that have been identified in a gene. If the need for a rapid time to result is clinically indicated, an assay may be designed to limit complexity, such as through targeted detection of a small number of the most common and clinically relevant variants. Commercially available IVDs are available for some pharmacogenetic applications and may reduce complexity of testing and data analysis in order to reduce the time to result. ^, However, most pharmacogenetic testing is based on laboratory-developed approaches performed at a central or reference laboratory. Clinical laboratories that offer pharmacogenetic testing can be found through the voluntary National Institutes of Health Genetic Testing Registry.

Clinical interpretation

Pharmacogenetic testing is clinically useful only when information is sufficient to allow clinical interpretation of the results. This information must be derived from in vivo human studies. Many examples of this type of information can be found in the peer-reviewed literature. One limitation of existing literature, however, is that most data are based on retrospective studies, and there is no single printed source in which all of this information has been collated. The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB) is a publicly available online research tool developed at Stanford University with funding from the National Institutes of Health and is part of the Pharmacogenetics Research Network (PGRN), a nationwide collaborative research consortium. ^, Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. This regularly updated database is an excellent source of genetic and clinical information.

Many ongoing clinical trials designed to study the efficacy and toxicity of new pharmaceutical products or new indications for previously developed pharmaceuticals have employed pharmacogenetic testing. Thus it is anticipated that pharmacogenetic guidelines, and possibly new companion diagnostics that would be simultaneously released to market with the pharmaceutical, will become available. In addition, drugs that were previously removed from development because of adverse drug reactions may be reconsidered if a genetic test can be demonstrated to identify individuals at high risk for adverse drug reactions, who could then avoid use of that drug. For each of the major genes discussed in this chapter, Table 73.3 provides a list of common drugs with pharmacogenetic associations that have resulted in several FDA-revised drug labels. ^, Because many other drug–gene combinations are recognized that may lead to additional drug label revisions, the discussion provided here is in no way comprehensive. In addition, many of the specific genes discussed later have applications to other areas of medicine, some of which are mentioned briefly. The European Medicines Agency has included pharmacogenetic information in drug labeling as well. While not all European countries participate, the European Union has promoted standardization in labeling of pharmaceuticals and included pharmacogenetic information in the summary of product characteristics. Table 73.4 provides examples of the sections in a European drug label that may include pharmacogenetic information and examples of genes that are targeted in drug labels. The specific examples discussed below can be used as a guide for translating the principles of pharmacogenetics to additional gene–drug pairs in this continually evolving field of laboratory medicine.

Pharmacokinetic associations