2024 Pharmacogenomics Lecture Notes PDF

PHARMACOGENOMICS Block: Foundations Block Director: James Proffitt, PhD Session Date: Tuesday, August 27, 2024 Time: 11:00 am - 12:00 pm Instructor: Todd Vanderah, PhD Department: Pharmacology Email: vanderah@arizona....

PHARMACOGENOMICS Block: Foundations Block Director: James Proffitt, PhD Session Date: Tuesday, August 27, 2024 Time: 11:00 am - 12:00 pm Instructor: Todd Vanderah, PhD Department: Pharmacology Email: [email protected] INSTRUCTIONAL METHODS Primary Method: IM13: Lecture ☐ Flipped Session ☐ Clinical Correlations Resource Types: RE18: Written or Visual Media (or Digital Equivalent) INSTRUCTIONS Please read lecture objectives and notes prior to attending session. READINGS N/A LEARNING OBJECTIVES 1. Define pharmacogenetics and pharmacogenomics. 2. Describe specific inherited traits that influence drug metabolism in a clinically significant fashion. 3. Summarize the major mechanisms (i.e., metabolism, enzymes, receptors) through which genetic variation can alter responses to drugs. Give examples of each. 4. Describe the potential outcomes of genetic variations and the use of medications CURRICULAR CONNECTIONS Below are the competencies, educational program objectives (EPOs), block goals, disciplines and threads that most accurately describe the connection of this session to the curriculum. Related Related Competency\EPO Disciplines Threads LOs COs CO-01 LO #1 MK-01: Core of basic sciences Pharmacology N/A CO-01 LO #2 MK-06: The foundations of Genetics EBM: Patient therapeutic intervention, Safety including concepts of outcomes, treatments, and prevention, and their relationships to specific disease processes CO-02 LO #3 MK-06: The foundations of Pharmacology H & I: Human therapeutic intervention, Development/Life including concepts of cycle outcomes, treatments, and prevention, and their relationships to specific disease processes Block: Foundations | VANDERAH [1 of 11] PHARMACOGENOMICS CO-02 LO #4 PBLI-07: Obtaining information Pharmacology EBM: Patient about the populations and Safety communities from which individual patients are drawn and applying it to the diagnosis and treatment of those patients INTRODUCTION Scientists and physicians are increasingly aware that genetic variations can cause different patients to respond in different ways to the same medication. The study of how genes affect the way a patient responds to drugs is called pharmacogenetics or pharmacogenomics. Although definitions differ, the term pharmacogenetics most commonly refers to the study of the relationship between individual gene variants and variable drug effects. In contrast, pharmacogenomics involves the study of the relationship between variants in a large collection of genes, up to the whole genome, and variable drug effects. For the purposes of this lecture, pharmacogenomics will be used as an inclusive term referring to both pharmacogenetics and pharmacogenomics. Until recently, physicians have used a “one-size-fits-all” approach to prescribing medicines. They usually started with standard doses of drugs and observed how patients responded. If necessary, the physician then changed the dose or drug by “trial and error”. Physicians didn’t understand why some patients experienced serious adverse effects from a particular drug or why certain medications weren’t effective in a percentage of patients. The concept of pharmacogenomics is basically “one size does not fit all” in regard to prescribing medicines for patients. Pharmacogenomics is a subset of precision medicine, which is the concept of prevention and treatment strategies that take individual variability into account. GENETIC VARIATION AND RESPONSE TO DRUGS There is great heterogeneity in the way individuals respond to drugs, both in terms of toxicity and treatment efficacy. Potential causes for variability in drug effects include factors such as environment, age, gender, ethnic group, liver function, kidney function, concomitant illnesses, and nutritional status. It is now well recognized that inherited differences in the metabolism and disposition of drugs, as well as targets of drug therapy (e.g. receptors), can have a profound influence on the efficacy and toxicity of medications. As shown in Figure 1 (and described in recent lectures), two distinct processes, either of which can be influenced by genetic factors, underlie the generation of a clinical drug action: 1) delivery to, and removal from, target sites in plasma on cell surfaces, or within cells (pharmacokinetics) and 2) interaction with the targets to generate a cellular effect that is translated to a clinical effect (pharmacodynamics). Thus, the starting point for many genetic studies is identification of variable drug responses in an individual patient or across a population. Then, an understanding of the underlying pharmacokinetics or pharmacodynamics can be used to identify individual candidate genes in Block: Foundations | VANDERAH [2 of 11]  PHARMACOGENOMICS which alternate function may “explain” the variable drug response. Recent studies have emerged in order to identify many candidate genes or even the whole genome for explained differences in responses to medications. Figure 1. Overview of pharmacokinetics and pharmacodynamics. Pharmacokinetic properties influence the availability of the drug in the system. Pharmacodynamics determines the drug effect. FOUNDATIONS OF PHARMACOGENOMICS The belief that inter-individual variation in the efficacy and toxicity of drugs is determined by inherited (i.e., genetic) factors is derived from studies of twins. These studies showed that the plasma half-lives of some drugs are very similar in monozygotic twins but much more variable in dizygotic twins, siblings, and the population in general. The framework for the discovery of genetic traits was based on phenotypic differences among individuals in a population. Some population dose-response curves revealed discontinuous variation suggesting that the population consists of two different types of individuals with regard to the property studied, i.e., a bimodal distribution of responses (Figure 2). Recall that when the number of individuals responding in a particular fashion is expressed graphically (frequency distribution), the pattern of responses generally follows a normal distribution curve. Some persons will be more sensitive to the drug and some will be less sensitive, but the spectrum of responses usually follows a unimodal distribution (Figure 2). Figure 2. Population dose response curves. In the bimodal example in Figure 2, approximately 40% of the population responds to the drug at a significantly smaller dose. Studies have demonstrated in many cases that the basis of these phenotypic differences is variation in the genomes between individuals. Block: Foundations | VANDERAH [3 of 11] PHARMACOGENOMICS A good example of this is determining whether a patient is a fast acetylator or a slow acetylator (Figure 3) Figure 3. Differences in rates of acetylation. From: Strachan, T. et al. (2015) Genetics and Genomics in Medicine, Garland Science The graph above shows an example of a biphasic distribution of plasma concentrations in patients who were administered the drug isoniazid, a drug for the treatment of tuberculosis. Isoniazid must be acetylated to be eliminated from the body by the Phase II metabolic pathways. Patients characterized as fast acetylators, are homozygous for the normal allele of the gene NAT2, which encodes the enzyme N-acetyltransferase II. However, those patients who carry a variant of NAT2 are slow acetylators, eliminating the drug at a much lower rate. Why is this important?? Well the patients with a slower rate of elimination have a much higher incidence of toxic side effects (the drug isoniazid will accumulate in the body). So if you decide to lower the dose for all patients to reduce toxicity, what happens to the patients that are fast acetylators??? Moreover, this same enzyme system (NAT2) is involved in the elimination of certain carcinogens, which are produced during cooking of meat at high temperatures; patients with this NAT2 gene variant have shown higher incidences of bladder cancer. The most common type of variation is a change in a single nucleotide pair termed a single nucleotide polymorphism or SNP (pronounced “snip”) (For Review see Dr. Bear’s Lectures “Human Genome” and “Gene Expression”). Although the frequency of SNPs is high, only a small fraction of these millions of SNPs in the genome will have phenotypic importance. Block: Foundations | VANDERAH [4 of 11] PHARMACOGENOMICS EXAMPLES OF GENETIC VARIATIONS THAT INFLUENCE DRUG METABOLISM Polymorphisms in Cytochrome P450 (CYP) Genes Metabolism (biotransformation) of many medications from their “parent” form to an inactive form OR from their “prodrug” form to their active form is mediated by the cytochrome C P450 Phase I enzymes. Therefore, the genetic variations in these enzymes can have significant effects on medication efficacy and/or side effects. CYP2D6 - The first clinically apparent polymorphism of the cytochrome P450 (CYP) family of enzymes was reported for CYP2D6. During clinical studies of a sympatholytic anti-hypertensive agent (e.g., beta receptor blocker, metoprolol), investigators noted that individuals possessing a CYP2D6 polymorphism required a lower dose for blood pressure control. Subsequent studies demonstrated that this discrepancy was related to the extent to which the drug was metabolized. Subsequently, many other drugs (at present, >50) have been shown to be metabolized by CYP2D6 including several antidepressants, anti-psychotics, opioids and other drugs used in cardiology besides metoprolol. Most importantly, there are differences in the distribution of CYP2D6 alleles among different ethnic populations and standard doses of medications have been reported to result in increased rates of adverse drug reactions in poor metabolizers. CYP2C19 – A large number of drugs including proton-pump inhibitors, antidepressants, antiepileptics, and antiplatelet drugs are metabolized by cytochrome CYP2C19. As in the case above, large variations in metabolic rates can occur among different populations, but also between individuals within a single population. For example, the drug clopidogrel (Plavix), an antiplatelet drug prescribed to patients with coronary artery disease, is metabolized by CYP2C19 to an active form. Therefore, genetic polymorphisms in CYP2C19 can have a very large influence on the efficacy of antiplatelet activity in which incorrect dosages can be life-threatening. For example, low levels of CYP2C19 due to genetics would result in a patient needing higher doses of clopidogrel in order to prevent future coronary artery issues. At the same time these high doses of clopidogrel to a person with high levels of CYP2C19 expression may result in large amount of the active form resulting increased risk of bleeding. Block: Foundations | VANDERAH [5 of 11] PHARMACOGENOMICS CYP2C9- Along these same lines the genetic polymorphism of the CYP2C9 and/or vitamin K epoxide reductase complex 1 (VKORC1) will have a very large role on the efficacy of the drug Warfarin (Fig. 4). Warfarin has a very narrow therapeutic index (thought to be responsible for 30% of adverse events) and becomes even more dangerous in patients that have a polymorphism in either of these enzymes; hence the standard recommended dose accidently given to a patient with a polymorphism of CYP2C9 or VKORC1 will result in a significant decrease in clearance and increased risk for bleeding. Hence, knowing that a patient may have a polymorphism in either of these enzymes will require a lower dose of Warfarin to avoid complications. Figure 4. Schematic demonstrating how Warfarin acts to inhibit VKORC1, an enzyme necessary to generate the active clotting factors. Hence, Warfarin is an anticoagulant that is metabolized mainly by CYP2C9. Polymorphisms of CYP2C9 or VKORC1 can result in higher levels of S-Warfarin that can cause severe bleeding. Genetic variations also occur in the “Phase II” of biotransformation. One example was listed above in Figure 3 with slow and fast acetylators and NAT2 expression levels. Another great example that you should be aware of is the genetic variation in the expression of a glucuronic transferase enzyme. UGT1A1 – The gene UGT1A1 encodes uridine 5’-diphosphoglucuronosyl transferase, which conjugates glucuronic acid onto small naturally occurring lipophilic molecules (e.g. bilirubin); however, the enzyme also modifies a wide variety of lipophilic drugs facilitating their excretion into the bile. A number of alleles of UGT1A1 found in different populations cause a wide variation in the elimination efficiency of these drugs, and patients with these alleles are at great risk for severe toxicity. An example is the commonly used chemotherapeutic agent, Irenotecan (Camptosar), which is an inhibitor of topoisomerase 1, which is required for DNA replication. Irenotecan is a prodrug and is metabolized to its cytotoxic active form. Cancer patients with specific variants in UGT1A1 are unable to eliminate the active form of irenotecan resulting in life-threatening toxicities. The availability of rapid, easy and cost-effective genotyping assays are beginning to influence therapeutics and clinical trial/drug development strategies. The resulting variations in the activity of Phase I enzymes leads to classification of individuals into the following categories: poor (PM), intermediate (IM), extensive (EM) and ultra-rapid (UM) metabolizers. Knowing this Block: Foundations | VANDERAH [6 of 11] PHARMACOGENOMICS information for each patient begins to “frame” the idea of Precision Medicine or Personalized Medicine. Human Response to Succinylcholine Succinylcholine is a neuromuscular blocking drug used to induce skeletal muscular relaxation in a variety of clinical applications, but most often for tracheal intubation (placement of a tube in the trachea of a patient for mechanical ventilation). The advantage of the drug over curare-like drugs is its rapid onset and extremely short action. The duration of action is short because plasma cholinesterase (often termed pseudocholinesterase) rapidly hydrolyzes the choline diester to succinylmonocholine (inactive) and then to choline plus succinic acid. In rare instances, patients have a prolonged response to succinylcholine, hours instead of minutes which can A. Pseudocholinesterase Outcome: Succinylcholine (in serum) cause prolonged apnea. Succinylmonocholine Muscle relaxant Acetylcholinesterase (inactive) (≈5 mins) Biochemical studies (in neuromuscular junction) revealed that the prolonged Pseudocholinesterase B. response to succinylcholine (in serum) Outcome: Deficiency due to SNP is due to the presence of an Succinylcholine Prolonged mu scle Slower formation of Acetylcholinesterase relaxation (severe apnea) Succinylmonocholine atypical plasma (in neuromuscular junction) (inactive) cholinesterase. The enzyme is present in normal Figure 5. (A) Normally succinylcholine, a neuromuscular blocker, is rapidly metabolized by both pseudocholinesterase that is found in the serum and by acetylcholinesterase found at the neuromuscular amounts but differs from the junction to the inactive form (succinylmonocholine). (B) Patients with a SNP in the pseudocholinesterase have a poorly functioning enzyme that result in a significant increase in the ½ life of the drug that could typical enzyme in its ability result in the loss of the ability to breath along with sustained paralysis. to hydrolyze succinylcholine (Fig. 5). Family studies indicate that the presence of the atypical cholinesterase is a genetically determined characteristic. In the US population, the homozygous state for the atypical cholinesterase occurs in about 1:3000 persons. A SNP in the gene for human plasma cholinesterase is responsible for the production of the atypical cholinesterase. A SNP is a single nucleotide polymorphism. The SNP for the atypical cholinesterase is a change in an acidic amino acid to a neutral amino acid, which accounts for the reduced affinity of the atypical cholinesterase for choline esters. In clinical practice it is not necessary to phenotype persons for cholinesterase type but rather the use of succinylcholine is based upon patient and family history. If there is doubt, there are alternative agents available. EXAMPLES OF OTHER GENETIC VARIATIONS THAT INFLUENCE DRUG EFFICACY Glucose-6-phosphate Dehydrogenase (G6PD) Deficiency Over forty years ago, it was discovered that in susceptible subjects the antimalarial drug primaquine caused hemolytic anemia (abnormal breakdown of red blood cells). The condition Block: Foundations | VANDERAH [7 of 11] PHARMACOGENOMICS was found to be an X-linked inherited condition that typically affects men. It is estimated that 200 million people worldwide carry polymorphic genes for G6PD deficiency. In molecular genetic studies, the hemolytic anemia is associated with amino acid substitutions in the G6PD enzyme that result from single nucleotide polymorphisms. More than 400 apparent genetic variants have been identified that are associated with variable responses to oxidative stress in red blood cells. Approximately 11% of African-Americans have a variant of G6PD (termed A-), which makes them vulnerable to hemolysis caused by pro- oxidant drugs such as the antimalarial drug, primaquine. Different variants are present in other ethnic groups (such as Sardinians, Greeks, and Iranians) that confer even greater sensitivity to primaquine. Because primaquine sensitivity is inherited by a gene on the X chromosome, hemolysis is often of intermediate severity in heterozygous females who have two populations of red blood cells. More than 50 drugs may cause hemolysis in susceptible individuals with G6PD deficiency. Interestingly, individuals with some of these same G6PD gene variants are highly sensitive to oxidative quinone compounds found in fava beans, a common food in many parts of Asia and Africa, and have high rates of a hemolytic disorder termed “favism.” Genetic Polymorphism in a transporter for statins SCLO1B1 – The gene SCLO1B1 encodes the organic anion transporter OATP1B1. This transporter is located on the sinusoidal membrane (at the blood side) of hepatocytes and is critical for drug uptake in the liver, where a large number of drug metabolic transformations take place. There are several SCLO1B1 gene variants that have significant effects on drug uptake. An important example is the uptake of statins, an HMG-CoA reductase inhibitor that reduces cholesterol synthesis, and is prescribed to millions of patients across the world to reduce cardiovascular events due to atherosclerosis associated with hypercholesterolemia. Variants in SCLO1B1 with reduced organic anion transport capacity lead to enhanced plasma concentrations of some statins. Higher plasma statin levels are associated with adverse reactions, including muscle pain and weakness. It is relatively common to encounter patients with these SCLO1B1 variants, with great effort to discover alternative cholesterol-lowering drugs. Genetic Polymorphisms in Drug Receptors The use of molecular genetic techniques is beginning to reveal the genetic determinates of responsiveness to commonly used drugs. The beta-2-adrenergic receptor (B2AR) agonists are the most widely used drugs in the treatment of bronchoconstriction during asthmatic attacks. Two polymorphic loci within the coding region of the B2AR have been described at amino acids 16 and 27. Subjects with different genotypes for the polymorphisms of the B2AR show differences in the responsiveness of the airways to the inhaled beta-2-agonist (bronchodilator) albuterol. The clinical significance of the differences in the response to beta-2-agonist drugs in asthmatic patients is currently the subject of numerous studies, not to mention much debate. Block: Foundations | VANDERAH [8 of 11] PHARMACOGENOMICS Genetic polymorphisms are identified for the ryanodine (RYR1) receptor located in skeletal muscle (on sarcoplasmic reticulum and controls calcium levels in skeletal muscle) which can lead to malignant hyperthermia in the presence of several drugs including the volatile anesthetics and some muscle relaxants. Malignant hyperthermia is life threatening that can be prevented by using a ryanodine receptor antagonist called dantrolene. In clinical practice it is necessary to try and determine whether such phenotype exists based upon patient and family history prior to using volatile anesthetics or muscle relaxants. THE CLINICAL CONSEQUENCES OF GENETIC VARIATIONS The genomic variations in the genes that impact drug efficacy and toxicity demonstrate the importance of knowing the genotypes before initiating therapy. A very large number of people carry at least one clinically actionable drug metabolism or receptor gene variant. There are over 2 million serious adverse non-recreational drug reactions, which account for 5-7% of all hospital admissions. Approximately 4% of newly marketed drugs are ultimately removed from the market due to adverse effects. The table below lists some examples of severe drug-induced injuries or toxicities that are associated with gene variants. (you do not need to memorize all of these but being aware of these will be important to your practice as a future physician). From: Strachan, T. et al. (2015) Genetics and Genomics in Medicine, Garland Science Block: Foundations | VANDERAH [9 of 11] PHARMACOGENOMICS An important aspect of pharmacogenomics is differences across different populations in pharmacologically important gene variants. A key aspect of genomic medicine is to identify the ancestry of the patient in the earliest stages of treatment. Databases exist that link pharmacologically important gene allele frequencies with different populations, and can provide the physician and the pharmacist with critical information about possible adverse effects. With a growing awareness of the importance of pharmacogenomics in pharmacotherapy, the sequencing of a patient’s genome early in life will become an essential component of precision medicine. In Summary genetic variations can alter responses to drugs in multiple ways including drug metabolism, drug excretion, the drug’s efficacy and the adverse drug reactions that may occur. Pharmacogenomics will ultimately begin to change how individual patients are being treated THE USE OF PHARMACOGENOMICS IN CLINICAL DECISION MAKING There are a number of pharmacogenomics databases that can be used to look for genetic variants in genes associated with the pharmacokinetics and pharmacodynamics of many drugs. (http://www.pharmacogenomics.mc.vanderbilt.edu/pharmaco.php). Banner University Medical Center and the University of Arizona Health Sciences Center were recently awarded a National Institutes of Health grant as part of the “ALL OF US” precision medicine initiative to focus on the development of an electronic medical record system that will contain the genomic sequences of 150,000 patients and will enable scientists to better understand the relationship between the genome and human health and disease. Physicians will be able to use the EMR database to practice precision medicine and to employ pharmacogenomics in clinical decision making. There is a change under way from the traditional strategy to develop medications good for everyone. This may have served well for pharmaceutical company marketing but observations from dose-response studies suggest that society was not so well served. The genetic diversity of humans mandates change in the ways in which drugs are developed and utilized. Patients will benefit from improved drug safety and efficacy. During the next decade, an expansion of pharmacogenomic knowledge will occur and probably alter dramatically the way physicians prescribe drugs. Example Protocol; when seeing patients with need for pain meds Screening Questions: 1) Have you had any problems with medications in the past? 2) Do you consider yourself “sensitive” or “resistant” to medications? 3) Have you had any problems with medications in the past (Doctor or Dentist office) Block: Foundations | VANDERAH [10 of 11] PHARMACOGENOMICS Tests to Order: 1) Urine Drug Test (UDT) to determine current med metabolism, 2) Pharmacogenetics test Action items pending test results: 1) if 2D6 deficient, consider hydromorphone, oxymorphone, morphine, tapentadol 2) If the patient is CYP3A4 deficient, avoid fentanyl due to risk of accumulation/overdose 3) if OPRM1 is poorly functioning, no opioids will work well, this patient needs aggressive multidisciplinary preoperative management, consider kappa opioid 4) If UGT2B7 is poor, use of morphine may lead to opioid hyperalgesia Block: Foundations | VANDERAH [11 of 11]