Pharmacogenomics Module 01: Principles & Perspectives II PDF

Pharmacogenomics Module 01: Principles & Perspectives II Leniza G. De Castro-Hamoy, MD, FPPS | Asynchronous TABLE OF CONTENTS I. BACKGROUND AND RATIONALE........................................................1 A. GAPS IN PHARMACOLOGIC THERAPY.......................................... 1 B. PHARMACO...

Pharmacogenomics Module 01: Principles & Perspectives II Leniza G. De Castro-Hamoy, MD, FPPS | Asynchronous TABLE OF CONTENTS I. BACKGROUND AND RATIONALE........................................................1 A. GAPS IN PHARMACOLOGIC THERAPY.......................................... 1 B. PHARMACOGENOMICS................................................................ 1 C. GOAL OF PHARMACOGENOMICS.................................................1 D. INDICATIONS FOR PHARMACOGENOMIC STUDIES......................1 E. HUMAN GENOME PROJECT OF 2003........................................... 2 II. REVIEW OF BASIC CONCEPTS........................................................... 2 A. DEFINITIONS AND NOMENCLATURE............................................2 B. COMMON FORMATS TO REPRESENT VARIABILITY OF A SPECIFIC GENE................................................................................................ 3 III. APPLICATIONS................................................................................ 3 A. PHASE I ENZYMES: CYP2D6..........................................................3 Figure 1. Other factors that affect drug response B. PHASE II ENZYMES: THIOPURINE S METHYLTRANSFERASE (TPMT)............................................................................................. 4 C. POLYGENIC EFFECTS: CYP2C9 AND VKORC1.................................4 IV. LOCAL RESEARCH............................................................................5 QUESTIONS......................................................................................... 5 ANSWER KEY.......................................................................................6 RATIONALE..........................................................................................6 LEARNING OBJECTIVES 1. Describe basic pharmacogenomic terms and principles 2. Give examples of polymorphisms and their impact on pharmacokinetics and/or pharmacodynamics 3. Identify potential aspects in research both locally and internationally I. BACKGROUND AND RATIONALE A. GAPS IN PHARMACOLOGIC THERAPY ● Drugs will not work for everyone ○ Some drugs for non-communicable diseases (i.e. hypercholesterolemia, asthma, or mental health conditions) will only work in 1/4 or even 1/25 of patients ○ Great variability in response ● Drugs cause adverse drug reactions in some patients ○ Comes in 2 forms: ▸ Drug misuse ⎻ Taking too much medication ⎻ Taking medication for too long or too often ▸ Idiosyncratic ⎻ Mysterious and very hard to predict ⎻ Observed to be the result of individual variations encoded in the genome ○ Genetic variation in genes for drug-metabolizing enzymes, drug receptors, and drug transporters have been associated with individual variability in the efficacy and toxicity of drugs ○ However, there are several other factors that can affect drug response YL6:01.23 B. PHARMACOGENOMICS ● The study of genetic factors that underlie variation in drug response ● Pharmacogenomics has replaced the term pharmacogenetics ○ More than one genetic variant may contribute to variation in drug response ○ Genetics: looks into the function and composition of a single gene ○ Genomics: addresses all genes and their relationships ▸ To identify the combined influence on the growth and development of an organism ● Predicts who the drugs will work for and who will get adverse reactions ○ Genetics is one of the many factors that may affect drug response C. GOAL OF PHARMACOGENOMICS ● Personalize medicine ● Maximize drug efficacy ● Minimize drug toxicity Take Note! ● “Five rights of medication use” ○ The right dose of ○ The right drug for ○ The right indication for ○ The right patient at ○ The right time ▸ D. INDICATIONS FOR PHARMACOGENOMIC STUDIES ● At this point in time, we do not test/study all patients taking all kinds of drugs ● Drugs with the following characteristics should be prioritized: ○ Narrow therapeutic index ○ High variability ○ Race differences ○ Significant safety concerns TG09: Barin, Choudhry, Cu, Jamisola, Sanota, Simbulan, So, Tagulob, Umil, Urrutia, Velasco, Yu CG01: Alvarez, Balayan, Bantayan, Cosico, Escalante, Majarais, Manlutac, Ozaeta, Rivera, Roque, Santiago 1 E. HUMAN GENOME PROJECT OF 2003 ● Even if studies and observations regarding pharmacogenomics began way before 2003, it was the completion of the human genome project which paved the way for advances in this field Active Recall Box 1. What is the most common kind of polymorphism? 2. What is the pharmacogenomic significance of the answer to the question above? Answers: 1 SNPs -Single nucleotide polymorphisms, 2 They can help predict the variability of an individual’s response to a drug II. REVIEW OF BASIC CONCEPTS A. DEFINITIONS AND NOMENCLATURE Figure 3. Metabolizer phenotypes CHROMOSOME ● Humans normally have 2 copies of every chromosome ○ Therefore, humans have 2 copies of each gene ● Each chromosome is composed of one large continuous DNA molecule (01.29, 2025) ALLELE Figure 2. Chromosome to Gene to Protein ● One or two more alternative forms of a gene found at the same genetic locus ○ E.g. CYP2D6*3 – important variant allele of CYP2D6, a drug-metabolizing enzyme ● An individual inherits two alleles for each gene, one from each parent ○ Homozygous: two alleles are the same ▸ E.g. CYP2C19*1/*1 ⎻ Have this gene on both copies ○ Heterozygous: two alleles are different ▸ E.g. CYP2C19*1/*2 ⎻ One copy is star 1, the other copy is star 2 GENE HAPLOTYPE (01.21, 2026) ● Basic physical and functional unit of heredity ● Segment of DNA that encodes a protein product (01.21, 2026) ● Series of alleles found in a linked locus on a chromosome ● Set of DNA variations or polymorphisms that tend to be inherited together ● May also refer to a combination of alleles or to a set of single nucleotide polymorphisms (SNPs) found on the same chromosome GENOTYPE ● Individual’s collection of genes ● May impact drug metabolism ○ CYP2C19*1/*1 – normal activity ○ CYP2C19*1/*2 or *1/*3 – reduced activity ○ CYP2C19*2/*2, *2/*3, or *3/*3 – no activity due to absence of wild-type/normal gene *1 GENOME ● Composed of: ○ Approximately 20,000 protein genes ○ Non-coding RNAs ○ Pseudogenes PHENOTYPE ● A clinical presentation or observable characteristics of an individual with a particular genotype ○ E.g. poor, ultrarapid, intermediate, or normal metabolizer phenotype (see Figure 3) ▸ Effect on drug metabolism will still depend on whether it acts on the active drug or prodrug YL6:01.23 Pharmacogenomics POLYMORPHISMS ● Variation in a gene, DNA sequence, or chromosome ● Variations in a population ○ Polymorphism: found in >1% of the population ○ Mutation: found in <1% of the population Single Nucleotide Polymorphism (SNP) ● Most common type of genetic variation among people ● Type of polymorphism involving variation in a single base pair in the human genome ○ Each SNP represents a difference in a single DNA building block or nucleotide ● Occur normally in a person’s DNA ○ 1 SNP in every 1,000 nucleotides on average ▸ Approximately 4-5 million SNPs in an individual’s genome ○ Variations may be unique to an individual or generally common ▸ There are over 100 million known SNPs globally ● SNPs help predict an individual’s response to certain drugs ● Effect on protein synthesis 2 ○ Non-synonymous polymorphism ▸ May cause a premature stop and alter protein synthesis ○ Synonymous polymorphism ▸ May not alter protein synthesis III. APPLICATIONS A. PHASE I ENZYMES: CYP2D6 ● Phase I enzymes ○ Involved in biotransformation of more than 75% of prescription drugs ▸ Polymorphisms in these enzymes may significantly affect blood levels which may alter response to many drugs [Case #1] Codeine and Cytochrome P450 and CYP2D6 Figure 4. SNP Replaces Nucleotide Adenine (A) With Cytosine (C) B. COMMON FORMATS TO REPRESENT VARIABILITY OF A SPECIFIC GENE SNP NOMENCLATURE ● Format: <GENE> <nucleotide position in the gene> <original wild-type nucleotide> <change in the sequence> ● E.g. VKORC1 1173 C>T ○ Gene name italicized and capitalized: VKORC1 ○ Nucleotide position: 1173 ○ Original wild-type nucleotide and change in sequence: C>T ▸ Cytosine became thymine ● Codeine is a commonly used opioid ○ It’s a prodrug ○ Must be metabolized into morphine for activity ● CYP2D6 ○ Part of the CYP450 enzymes ○ Metabolizing enzyme for codeine found in the liver ▸ Missing CYP2D6 gene → codeine does not work effectively ○ Based on function of CYP2D6 on codeine, a prodrug ○ Normal CYP2D6 function → normal morphine concentration ○ Increased function of CYP2D6 → proportional increase in the morphine concentration ▸ Expect high active drug, morphine concentration ○ Decreased function of CYP2D6 → lower morphine concentration ▸ CYP2D6 is not enough to transform the prodrug into the active drug REFERENCE SNP (rs) ● Based on the dbSNP (SNP database) ● Central database for nucleotide variations ● Access to database: https://www.ncbi.nlm.nih.gov/snp/ STAR ALLELE NOMENCLATURE ● Format: <GENE> <*allele number> / <*allele number> ● E.g. CYP2C19*1/*2 ○ Gene name italicized and capitalized: CYP2C19 ○ Inherited allele numbers: *1/*2 ▸ *1: normal (wild-type) activity ▸ *2: no enzymatic activity ○ NOTE: functional outcomes designated per *# vary according to different genes ▸ i.e. *1 is not always the wild-type allele Active Recall Box 1. T/F: Genotype is the basic and physical functional unit of heredity 2. What type of polymorphism may cause a premature stop and an alteration in protein synthesis? A. Synonymous polymorphism B. Non-synonymous polymorphism C. NOTA Answers: 1F, 2B YL6:01.23 Pharmacogenomics Figure 5. Impact of Variable Pharmacokinetic Gene Function on the Effects of Bioactivation of Prodrug Versus Inactivation of an Active Drug ● Thiopurine S-methyltransferase (TPMT) ○ Function of TPMT is on azathioprine or 6-mercaptopurine ○ Normal function of TPMT → expected drug effect ○ If decreased function of TPMT → risk of hematological toxicity ○ No function of TPMT → high risk of hematological toxicity ▸ Drug just accumulates since it is not being metabolized 3 EFFECT OF METABOLIC RATE ON DRUG DOSAGE Table 1. Effect of Metabolic Rate on Drug Dosage Phenotype Poor metabolizer Ultra-rapid metabolizer Prodrug Active Drug ● Poor efficacy ● Possible accumulation of prodrug ● Good efficacy ● Accumulation of active drug can produce ● May need to lower dose ● Good efficacy ● Rapid effect ● Poor efficacy ● Need greater dose or slow-release formulation B. PHASE II ENZYMES: THIOPURINE S METHYLTRANSFERASE (TPMT) [Case #2] 6-Mercaptopurine (6-MP) and TPMT Nice! ● There are other alleles for decreased TPMT enzyme activity like *2, *3A, *3B, *3C ○ *3C was chosen because it’s most common in Asian populations TPMT IN SOUTH ASIA ● In a study on TPMT alleles of different ethnic populations, South-east Asians showed to have TPMT*3C as a deficiency allele ○ This was found in a Filipino patient Figure 7. Frequency of Variant TPMT Alleles in Different Ethnic Populations C. POLYGENIC EFFECTS: CYP2C9 AND VKORC1 [Case #3] Warfarin ● Oral anticoagulant, widely used to prevent and treat thromboembolic disease in patients with deep vein thrombosis (DTP), pulmonary embolism, mechanical heart valves and atrial fibrillation ● Associated with significant risk of major and sometimes fatal bleeding events MAINTAINING WARFARIN THERAPEUTIC RANGE IS CRITICAL Figure 6. Pathway of Azathiopine and 6-Mercaptopurine ● Azathioprine and 6-MP share the same metabolic pathway ● Azathioprine is a pro-drug of 6-MP ● 6-MP is used in treating immunological disorders ○ It is an anti-cancer agent ○ Activated by the salvage pathway ▸ Using enzyme: Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase) ▸ Forming product: 6-Thioguanine Nucleotides (6-TGN) ● 6-TGN is responsible for the therapeutic efficacy and the bone marrow toxicity ● 6-MP may be inactivated by TPMT or Xanthine Oxidase (XO) enzymes 6-MP AND TPMT ● If already inactivated by TPMT: 6-MP gives less adverse effects and toxicity ● Thus, if normal TPMT activity: expect less toxicity from 6-TGN ● TPMT*1: normal TPMT enzyme activity ● TPMT*3C: decreased TPMT enzyme activity ○ Increased 6-MP concentrations ○ Increased toxicity risk (myelosuppression) ○ Dose reduction is needed YL6:01.23 Pharmacogenomics ● The international normalized ratio (INR) must be kept within the target therapeutic range ○ Low INR leads to an increased risk of thromboembolic events ○ If INR becomes too high, there is an increased risk of bleeding Figure 8. Relationship between INR control and outcomes WARFARIN METABOLISM ● Metabolism of Warfarin takes place in the liver ○ The liver takes it up and metabolizes it with CYP450 enzymes ● Warfarin is a racemic mixture of R-warfarin and S-warfarin ○ S-warfarin is the more potent component and is metabolized by CYP2C9 ● The action of Warfarin is mediated by the inactivation of VKOR (Vitamin K Epoxide Reductase) enzyme ○ Has a role in the recycling of Vitamin K 4 ○ The recycling of Vitamin K is part of the coagulation process for coagulation factors II, VII, IX, and X ○ If the patient has the wild type allele for CYP2C9, then the patient can be started on a regular dose ○ The AA haplotype for VKORC1 necessitates a lower dose of warfarin of 3-4 mg VKORC1 IN DIFFERENT POPULATIONS ● Filipinos have a high frequency of the AA allele of VKORC1 ○ Recall: necessitates a lower dose of warfarin ● Important to check the patient’s genotype if possible to be more guided when starting medications Figure 11. VKORC1 alleles in Philippine population Figure 9. Warfarin Metabolism CYP2C9 ● Gene/allele: Cytochrome P450 2C9 ○ CYP2C9*1 wild type ▸ Normal function of CYP2C9 ▸ Results in normal Warfarin concentration ○ CYP2C9*2 variant allele ○ CYP2C9*3 variant allele FUNCTIONAL EFFECT ● CYP2C9*2 and *3 alleles result in: ○ CYP2C9*2: 50% decreased activity ○ CYP2C9*3: 90% decreased activity ● Decreased CYP2C9 activity results in increased warfarin concentrations POPULATION PREVALENCE ● Caucasians: 3-20% ● Asians & African-Americans: 1-4% Figure 12. Haplotype structure of the VKORC1 SNPs for the Asian populations Active Recall Box 1. The action of warfarin is also mediated by the inactivation of ____ which plays a role in the recycling of ___ 2. T/F: Group A haplotypes are associated with requiring higher warfarin dose 3. Which CYP2C9 allele results in a decrease in CYP2C9 activity by 90%? Answers: 1 VKOR; Vitamin K, 2F, 3CYP2C9*3 VKORC1 ● Gene/allele: Vitamin K epoxide reductase complex subunit 1 (VKORC1) ○ VKORC1 1173 C>T ○ VKORC1-1639 G>A (also known as 3673 G>A) ○ These two SNPs, along with others, combine to form several haplotypes FUNCTIONAL EFFECT ● Five common haplotypes are categorized into two groups, according to their impact on warfarin dose ○ Group A haplotypes (1 and 2): associated with requiring a lower warfarin dose ○ Group B haplotypes (7, 8, and 9) are associated with requiring a higher warfarin dose Figure 10. Estimated Warfarin Dose (mg/day) based on Genotypes ● Figure 10 can be used as a guide to determine what warfarin dose to start a patient on should their genotype on both CYP2C9 and VKORC1 be known YL6:01.23 Pharmacogenomics IV. LOCAL RESEARCH ● Local research on SNPs regarding drug response ● E.g. Klotho variant rs36217263 associated with poor response to cardioselective beta-blocker therapy among Filipinos ○ Potential marker to aid in the management of hypertension ○ Deletion of at least one copy of allele A of rs36217263 is associated with poor response to beta-blockers ○ Observed among participants using cardioselective beta-blockers, but not carvedilol QUICK REVIEW QUESTIONS 1. This is the study of genetic factors that underlie varying responses to drugs and medication. A. Ethnopharmacology B. Pharmacogenomics C. Genopharmacology D. Pharmacogenetics 2. Drugs with the following characteristics should be prioritized in the study of pharmacogenomics EXCEPT: A. Wide therapeutic index B. High variability 5 C. Race differences D. Safety concerns 3. Polymorphisms are defined as a variation in a gene, DNA sequence, or a chromosome in ___% of the population. A. >1 B. <1 C. >0.1 D. <0.1 4. Which of the following indicates normal activity of a drug in an individual? A. CYP *1/*1 B. CYP *1/*2 C. CYP *2/*2 D. CYP *2/*3 5. Ignatius (23M) gets shot in the leg with a cannon ball. His chart says has a missing CYP2D6 enzyme. Which of the following will not work effectively in his body? A. Morphine B. Codeine C. Cocaine D. Methamphetamine 6. The TPMT*3C allele has a high frequency in southeast asian populations. This implies ____ TPMT enzyme activity which means ____ myelosuppression and toxicity risk. A. Decreased ; decreased B. Increased ; increased C. Increased ; decreased D. Decreased ; increased 7. Following the question above, a dose ____ of ___ is needed in southeast asian populations. A. Increase ; 6-TGN B. Increase ; 6-MP C. Reduction ; 6-TGN D. Reduction ; 6-MP 8. Warfarin is an oral anticoagulant used to prevent and treat thromboembolic events. It has two variants, the more potent of which is _____ and is metabolized by ______ A. R- warfarin ; CYP2C9 B. R- warfarin ; CYP1A1 C. S- warfarin ; CYP2C9 D. S- warfarin ; CYP1A1 9. Which of these variants will increase warfarin concentrations the most? A. CYP2C9*1 B. CYP2C9*2 C. CYP2C9*3 D. All of the above 10. Studies show that Filipinos have a high frequency of the AA allele of VKORC1. This indicates that we need a ___ starting dose of warfarin. A. Lower B. Higher C. Average D. None of the above YL6:01.23 Pharmacogenomics ANSWER KEY 1B, 2C, 3A, 4A, 5B, 6D, 7D, 8C, 9C, 10A RATIONALE 1. B. Pharmacogenomics. Pharmacogenetics typically refers to effects involving a limited number of genes, often involving drug metabolism, whereas pharmacogenomics involves the study of complex multigene patterns within the genome. Ethnopharmacology is the study of medicines derived from naturally occurring substances, traditionally used to heal specific groups of people in their respective cultures. 2. A. Wide therapeutic index. Drugs with a wide therapeutic index are more difficult to study as each of their effects may pose additional variability to the study. 3. A. >1%. Variations in a gene, DNA sequence, or chromosome in <1% of the population is called a mutation. 4. A. CYP *1/*1. Star allele nomenclature has this format where *1 = normal (wild type). Choice B indicates reduced activity, while choices C and D indicate no activity. 5. B. Codeine. CYP2D6 is an enzyme in the liver that gets metabolized into morphine. This prodrug is a commonly used opioid. 6. D. Decreased ; increased. 7. D. Reduction; 6-MP. TPMT clears 6-MP from the body. Decreased or impaired TPMT activity as seen in SEA populations means higher 6MP conversion to 6-TGN, and thus higher myelosuppression and toxicity. Reducing the 6-MP dosage will compensate for the reduced TPMT activity. 8. C. S- warfarin ; CYP2C9. R-warfarin is not as potent and is metabolized by CYP1A1, CYP1A2, and CYP3A4. 9. C. CYP2C9*3. CYP2C9*1 is the normal wild type allele. Having a CYP2C9*2 variant reduces CYP2C9 activity by 50% while the CYP2C9*3 variant reduces CYP2C9 activity by 90% and thus increases warfarin concentrations more. 10. A. Lower. The AA haplotype of VKORC1 necessitates a lower dose compared to the GG and AG haplotypes. Refer to Figure 10. REFERENCES REQUIRED 💻 Hamoy, L. (August, 2023). Pharmacogenomics [Video]. https://ateneo.instructure.com/courses/35153/discussion_topics/1011 475?module_item_id=1842534 📄 2025. 01.29: Pharmacogenomics by Hamoy, L., MD. 📄 ASMPH ASMPH 2026. 01.21: Pharmacogenomics by Hamoy, L., MD. Concerns and Feedback form: http://bit.ly/YL6CFF2027 How’s My Transing? form: https://bit.ly/2027YL6HMT Mid-Semester Evaluation form: https://bit.ly/2027YL6MidSem End-of-Semester Evaluation form: https://bit.ly/2027YL6EndofSem Errata Points Trackers: https://bit.ly/YL62027EPT YL6 TransMap: https://bit.ly/2027YL6TransMap 6 APPENDIX Appendix A. Pharmacogenomic Terms YL6:01.23 Pharmacogenomics 7