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Friday, March 23 - Introduction of Pharmacogenomics in Clinical Practice


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Introduction of Pharmacogenomics in Clinical Practice
0006-0000-18-004-L04-P | .1 CEU |
Melanie Felmlee, PhD

Published in: Health & Medicine
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Friday, March 23 - Introduction of Pharmacogenomics in Clinical Practice

  1. 1. Introduction to Pharmacogenomics in Clinical Practice Melanie Felmlee, PhD Assistant Professor, Pharmaceutics & Medicinal Chemistry Thomas J Long School of Pharmacy & Health Sciences University of the Pacific No conflicts of interest
  2. 2. Lecture Objectives 1. Define and apply the basic vocabulary of genetics 2. Differentiate between drug metabolism and drug target pharmacogenomics 3. Describe the molecular basis for genetic variation in drug metabolism and response for select gene- drug pairs 4. Describe the application of pharmacogenomics knowledge in clinical practice
  3. 3. Variability in Pharmacokinetics &Drug Response How do we determine a patient’s response?
  4. 4. Therapeutic Area Drug name Disease Response Rate Antipsychotic Haloperidol (Gendol) Schizophrenia 73% @ 1 yr 52% @ 2 yrs Antidepressant Citalopram (Celexa) Major depression 81% @ 24 weeks Antihypertensive Enalapril (Vasotec/Epaned) Mild to moderate hypertension 42.7% @ 1 yr Atenolol (Tenormin) Mild to moderate hypertension 35.4% @ 1 yr Oncology Paclitaxel (Taxol/Abraxane) Breast cancer 21% Gefitinib (Iressa) NSCLC 10% Variability in Drug Response Clin Thera (1998) 20 Psychopharmacol (1997) 12 BMJ (1997) 315 Clin Breast Cancer (2001) 1
  5. 5. Treatment Efficacy Drug Toxicity Pregnancy/lactation Disease severity/ progression Other drugs, illnessesGenetic make-up Age Gender Ethnicity Lifestyle Factors Contributing to Variable PK/PD Pharmacogenetics/Pharmacogenomics The role of genetics in drug disposition (ADME) and response Adherence
  6. 6. Pharmacogenetics/Pharmacogenomics • Focus on the role of human genetics and genome wide expression on individual variability in drug disposition and response • DNA polymorphisms • mRNA expression (transcriptome) • Application of genetic/genomic technologies to drug discovery and development • Identify genes the determine efficacy and toxicity • Identify new therapeutic drug targets
  7. 7. Application of Pharmacogenomics • “Pharmacogenomics has the potential to provide patient-specific data upon which selection of medications and doses can be individualized and optimized” – Johnson et al. (2002) How may drug labels contain pharmacogenomic information? PharmGKB
  8. 8. • Goal is to find clinically meaningful information that can impact patient care • Selection of the appropriate drug and dose to achieve a desired therapeutic outcome based on genetic information • Application of genetic information to describe the interindividual variability (PK/PD) observed in the clinical population • Need to understand basic genetic concepts in pharmacogenomics to interpret testing results Application of Pharmacogenomics
  9. 9. Central Dogma of Genetics/Genomics PHENOTYPE
  10. 10. Central Dogma of Genetics/Genomics • Nucleotides • Adenine, guanine, cytosine and thymine (uracil in RNA) • Semi-conservative replication • One old and one new strand in daughter cell • Errors in replication occur leading to mutations
  11. 11. • Mutation: Any change in an individuals DNA sequence • Frequency < 0.01 (rare) • Silent versus amino acid change • Insertions/deletions • Genetic polymorphism: common variation in the population • Frequency > 1% • Single nucleotide polymorphisms (SNPs) • ~10 million in human genome • Less than 1% alter protein function • Identified by rs# Mutations and Polymorphisms
  12. 12. Allele, Haplotype & Genotype • Allele: two or more alternate form of DNA at a given location (gene) • Major and minor alleles • Haplotype: set of DNA variations that are inherited together • Set of SNPs within the same gene • Genotype: the genetic constitution of an individual • Combination of two alleles for a given gene
  13. 13. Nomenclature • Every individual has two alleles for a given location 521 T → C 521T – Allele 1 (*1a) 521C – Allele 2 (*5) 521TC → *1a/*5 OATP1B1*1a/*5 SNP Haplotype Genotype Gene Nomenclature
  14. 14. • Pre-prescription analysis • Global versus individual genes • Which genome to analyze? • Patient • Disease (eg. Tumor) • Pathogen • FDA-approved diagnostic tests • dures/InVitroDiagnostics/ucm330711.htm • dures/InVitroDiagnostics/ucm301431.htm • Direct to consumer genetic tests Determination of Individuals’ Genotypes
  15. 15. • Phenotype: the observable expression of a genotype as a morphologic, clinical, biochemical or molecular trait • The activity of a drug metabolizing enzyme or transporter CYP2D6*5/*5 – genotype Poor metabolizer – phenotype • Observed phenotype may not always be predicted from genotype • Environmental factors, additional genes and DDIs may influence the observed phenotype Phenotype Prediction from Genotype
  16. 16. What is an allele? a. Any change in the DNA sequence b. Set of DNA variations that are inherited together c. Two or more alternate forms of a gene d. Observable expression of a genotype Question #1
  17. 17. Clinical Application of Pharmacogenomic Data Goal is to individualize therapy based on genotype to improve efficacy and reduce adverse events
  18. 18. • Variability in pharmacokinetics and pharmacodynamics • Different clinical consequences from genetic variations in drug metabolism enzymes or drug targets • Altered drug metabolism • Changes in plasma drug concentrations and exposure • Toxicity • Subtherapeutic concentration • Genetic variation in drug target • Altered efficacy • Identification of populations that would benefit from therapy • Toxicity at alternative gene target not involved in PK/PD Clinical Application of Pharmacogenomic Data
  19. 19. Variability in Pharmacokinetics Rowland and Tozer Clinical PK and PD: Concepts and Applications. 4th Ed. Range of enzyme activities leading to changes in Cl and Cmax
  20. 20. Pharmacogenetics of Drug Metabolizing Enzymes • Enzyme activity (phenotype) is related to specific genotypes • Reduced and nonfunctional alleles Pharmacogenomics: Applications to Patient Care (2009) 1st Ed
  21. 21. • Any genetic variability that affects drug response through a non-pharmacokinetic mechanism • Variability in response is not explained by differences in drug concentration caused by differences in drug metabolism/transport • Variants are not typically inactivating • Amino acid changes or expression changes • There are not two (or more) distinct population distributions as seen with DMEs or transporters • Polymorphisms explain distribution of response Drug Target Pharmacogenetics
  22. 22. • Candidate gene approach • Genes of interest are selected based on PK and pharmacology knowledge • SNPs are identified followed by functional analysis • Clinical outcome is assessed last • Genome-wide association study (GWAS) • Does not rely on knowledge of drug or disease • Test between 350K and 1M SNPs per subject • Comparison between two groups • Healthy versus disease • Adverse event vs normal • GWAS results must be confirmed in multiple populations Approaches to Study Drug Target PGx
  23. 23. • Four gene-drug pairs: • CYP2C19 and clopidogrel • CFTR and ivacaftor • G6PD and rasburicase • VKORC1/CYP2C9 and warfarin Discussion: • General drug information • Molecular basis for genetic variation • Phenotype assignments • Therapy recommendation based on genomic information • Clinical guidelines are published by the Clinical Pharmacogenetics Implementation Consortium (CPIC) Patient Care Applications of Pharmacogenetics
  24. 24. • CPIC is a shared project between PharmGKB and the Pharmacogenomics Research Network • CPIC publishes peer-reviewed, evidence-based guidelines to help clinicians understand how genetic test results should be used to optimize drug therapy • Guidelines can center on genes or gene-drug pairs • Underlying assumption is that pre-prescription genotyping will become more wide spread Resource links: Clinical Pharmacogenetics Implementation Consortium
  25. 25. • Information linking genotype to phenotype • Information about available genetic tests • Therapeutic recommendations based on genotype/phenotype • Standard system for assigning strength to each prescribing recommendation based on available literature data • Supplementary material contains additional details CPIC Guideline Format
  26. 26. CYP2C19 and Clopidogrel (Plavix)
  27. 27. • Prodrug that requires CYP2C19-mediated metabolism to form active metabolite • Utilized in patients with acute coronary syndromes (ACS) undergoing percutaneous coronary intervention (PCI) • Clinical evidence linking adverse outcomes to CYP2C19 genotype • Boxed FDA warning regarding decreased efficacy in poor metabolizers Clopidogrel
  28. 28. • 36 alleles have been identified • *1 is the major allele (normal function) • Two predominant nonfunctional alleles • *2 and *3 • *2 occurs in 15 % of Caucasians, and up to 35 % of Asians • One haplotype leading to ultra-rapid activity • *17 occurring in up to 25 % of Caucasians • CYP2C19 testing is recommended prior to initiation of Clopidogrel therapy • Determined by clinician CYP2C19 Gene Variation
  29. 29. Clinical PK Consequences of Genotype Clopidogrel Gong et al (2012) Eur Heart J
  30. 30. Clopidogrel CPIC Guideline: Genotype-phenotype Scott et al. (2013) CPT
  31. 31. Clopidogrel CPIC Guideline: Therapeutic Recommendations Scott et al. (2013) CPT
  32. 32. CPIC Guideline: Clopidogrel Dosing Algorithm Scott et al. (2013) CPTTeaching Tool
  33. 33. If a patient has a CYP2C19*2/*17 genotype, how would you classify their enzyme activity phenotype? a. Ultra-rapid metabolizer b. Extensive metabolizer c. Intermediate metabolizer d. Poor metabolizer Question #2
  34. 34. CFTR and Ivacaftor (Kalydeco)
  35. 35. • Cystic fibrosis (CF) is caused by autosomal recessive mutations in the CFTR gene • CFTR: CF transmembrane conductance regulator protein • CFTR is a bicarbonate and chloride transporter, and also regulates other transporters • CFTR is expressed in numerous tissues including airways and small/large intestine • In CF, defective CFTR results in absent chloride transport CFTR
  36. 36. CFTR Variants • Class I – III are considered nonfunctional and lead to severe disease • Class IV – VI have some residual CFTR function Clancy JP et al. (2014) CPT
  37. 37. CPIC Guideline for Ivacaftor • First drug on the market to target a specific CFTR defect • Approved in 2012 • Shown to increase chloride ion flow in G551D variants (Class III) • 2017 approval for treatment of additional mutations that result in a CFTR splicing defect (not covered in guideline) Clancy JP et al. (2014) CPT
  38. 38. CPIC: Dosing Guideline for Ivacaftor Clancy JP et al. (2014) CPT
  39. 39. Ivacaftor Prescribing Algorithm • Not a stand alone treatment • Patients likely need concomitant medication to address other disease manifestations Teaching Tool Clancy JP et al. (2014) CPT
  40. 40. G6PD and Rasburicase (Elitek)
  41. 41. • G6PD converts glucose-6-phosphate to 6- phosphogluconolactone and produces NADPH • In red blood cells, this is the only source of NADPH which is required to protect cells from oxidative stress • G6PD deficiency results in RBCs that are susceptible to drug-induced lysis • Methemoglobinemia: >1% methemoglobin in circulating blood G6PD
  42. 42. • G6PD is located on the X-chromosome • Males only have one copy of the gene • >80 variants described • Genetic variants are split into five classes (I – V) from most severe deficiency to highest enzyme activity • Class I: <10 % activity with hemolytic anemia • Class II: <10% activity • Class III: 10 - 60% activity • Class IV: normal activity • Class V: > normal activity G6PD Genetic Variation
  43. 43. CPIC Guideline for Rasburicase Rasburicase is a recombinant urate oxidase enzyme for the treatment of hyperuricemia during chemotherapy Label contains a black box warning for G6PD deficiency Relling MV et al. (2014) CPT
  44. 44. CPIC Guideline for Rasburicase Relling MV et al. (2014) CPT
  45. 45. CPIC: Dosing Guideline for Rasburicase Relling MV et al. (2014) CPT
  46. 46. CPIC: Rasburicase Dosing Algorithm Teaching Tool Relling MV et al. (2014) CPT
  47. 47. Select the appropriate genotype (based on WHO classifications) for ES (40 yo, female) who has a deficient glucose-6-phosphate dehydrogenase activity phenotype without hemolytic anemia. a) II b) II/II c) IV d) II/IV e) I/I Question #3
  48. 48. VKORC1/CYP2C9 and Warfarin
  49. 49. • Original publication in 2011 in CPT • Gage and IWPC algorithms • COAG trial: no difference between Pgx and non-genetic dosing algorithms during the first four weeks of therapy • EU-PACT trial: Pgx algorithm performed between in the first four weeks • GIFT trial: Pgx guided dosing reduced the combined risk of major bleeding • Algorithms outperform fixed dose and non-genetic algorithms except in those with African ancestry when only CYP2C9*2 and *3 are considered • Guideline update in 2017 to include recommendations based on an individuals continental ancestry Updated CPIC Guideline for Warfarin Dosing
  50. 50. • Fifty seven alleles have been identified • Two predominant reduced function alleles • *2 & *3 are found in 35% of Caucasians • Four additional reduced function alleles • *5, *6, *8, *11 • Highest frequency in individuals with African ancestry • Most FDA-approved clinical tests only include *2 and *3 CYP2C9 Gene Variation
  51. 51. • A common noncoding variant is significantly associated with warfarin sensitivity • -1639G>A • The polymorphism alters a transcription factor binding site resulting in lower protein expression • Several rare nonsynonymous variants confer warfarin resistance (high dose requirements) • Typically not evaluated in commercial tests VKORC1 Genotypes
  52. 52. CPIC Warfarin Dosing Recommendations Johnson JA et al. (2017) CPT
  53. 53. CPIC Warfarin Dosing Recommendations • contains both algorithms • CYP2C9*5 and *6 can be included Johnson JA et al. (2017) CPT
  54. 54. • Utility of pharmacogenomic information to understand patient variability prior to initiation of therapy • Drug and dosage selection • Identification of ‘responder’ or ‘ADR’ subpopulations • Molecular basis and clinical implementation for specific gene-drug pairs • Challenges to the widespread implementation of clinical pharmacogenomics data Summary & Perspectives
  55. 55. Questions?