PHARMACOGENOMICS. The Time is Now! Today you will learn to: 4/3/2018. Conflict of Interest Disclosure

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1 PHARMACOGENOMICS The Time is Now! Kathleen B. Orrico, PharmD, BCPS April 14 th 2018 Associate Professor of Pharmacy UCSF Conflict of Interest Disclosure I am affiliated with the University of California San Francisco, Stanford Center for Clinical Research, & Verity Health. I have no other commercial affiliations. Today you will learn to: 1. Gain a basic understanding of the interplay between the human genome & the sciences of pharmacology and pharmacokinetics. 2. Identify clinically actionable gene-drug associations after review of foundational pharmacogenomic (PGx) concepts and terms. 3. Identify and use reliable PGx resources. 4. Become inspired to seek the future! 1

2 If this is the future. Where is my jetpack? The Human Genome Complete set of genetic instructions or the *blueprint* for making every protein, cell, tissue, and organ of a human being. The molecular basis for inheritance, passed along at every cell division and to offspring. These directions are spelled out *encoded* in the sequence of nucleotide bases that comprise the molecule of deoxyribose nucleic acid >DNA. The Age of Personalized Medicine 1953 James Watson &Francis Crick worked with Maurice Wilkins & Rosalind Franklin. Discovered DNA as a double helix polymer 1977 Frederick Sanger discovered a means to sequence the base-pairs that comprise DNA. First human gene sequenced 1990 The Human Genome Project (BioProject) Completed in 2003 Worldwide effort to map the entire human genome & sequence the 2.91 billion base-pairs that spell out the genetic blueprint in the structure of DNA. 2

3 Genetics or Genomics? PharmacoGENOMICS (PGx) Knowing a person s gene variation helps us predict an individual s response to a drug, propensity for developing certain drug side effects, or variation in the rate and extent of drug metabolism. Personalized / Precision Medicine PharmacoGENETICS (PGt) Refers to a subset of PGx typically applied when referring to a single variation in a gene. Epigenetics ~Above or upon the gene The study of factors within the cell or the environment that influence the expression or suppression of genes. It s All About Protein! Enzymes Cytokines Cell Surface Components Protein Receptors Targets Hormones Transporters Genetic Variation Differences in the DNA base sequence can ultimately lead to variation in the structure or the amount produced of the encoded protein. DNA Genes Proteins 3

4 deoxyribonucleic acid (DNA) Single Strand View Double Helix Structure * Twisted Ladder Double stranded polymer of nucleotide base units. Side rails repeating units of the five carbon sugar deoxyribose linked by an acidic phosphate group. Rungs of the ladder - hydrogen bonding of two of four different nitrogenous bases. Credit: U.S. National Library of Medicine Nitrogenous Bases = The Code Purines Pyrimidines Adenine Guanine A G T C Thymine Cytosine Question? Given the base sequence in one strand, what is the complementary base sequence? Start Codon Leucine Aspartic Acid A T G C T GGA C T A C G A C C T G 4

5 Chromosomes Tightly coiled arrangements of sections of the DNA double helix strand. The complete genome (~3 billion base-pairs) is contained within the nucleus of every human cell except red blood cells, platelets, and gametes. (ndna) If uncoiled the ndna strand measures over 6 ft. Each chromosome can contain million base-pairs and hundreds to thousands of genes. Chromosomes 23 Pairs of Chromosomes 22 Autosomes -One from each parent. -Numbered largest to smallest. -Biallelic expression 1 Pair of Sex Chromosomes -X and Y 5

6 Telomeres Telomeres listen to you, they listen to your behaviors, they listen to your state of mind, said Blackburn, president of the Salk Institute for Biological Studies in La Jolla, Calif. Genes Genes are stretches of the DNA strand that encode for the amino acid structure and thus the function of proteins. ~20,000 Often named for the protein they encode. One gene may hold the recipe for one or hundreds of different proteins. Humans are diploid beings and have 2 copies of each gene. Alleles are different versions of a gene. (Symbol followed by an asterisk and the variant #) Definitions Wild Type Allele the form of a gene shared by many in a population. CYP2C19*1 or *1A Star Nomenclature The Pharmacogene Variation Consortium PharmVar 1 Central repository for CYP450 & PGx enzyme nomenclature. Genotype the specific combination of alleles an individual possesses. *1/*9, *1B/*8 Haplotype a group or set of the same alleles that are inherited as a set. Indicates common descent. Polymorphism multiple forms of a gene / protein Phenotype visible trait or characteristic resulting from gene expression. i.e. eye color, enzyme activity 6

7 Reliable Resources Basic Genetic Concepts Khan Academy khanacademy.org YouTube video lessons in basic genetics. Genetics Home Reference 2 US National Library of Medicine ghr.nlm.nih.gov Genetic Glossary for Definitions National Human Genome Research Institute 3 Talking Glossary genome.gov/glossary/ VIPs- Very Important Pharmacogenes Pharmacogenes encode for proteins involved in drug action, toxicity, or metabolism. Variation in pharmacogenes results from deletions, insertions, or substitutions within the usual or wild-type sequence of nitrogenous bases that comprise the gene. To date, the premier curators of pharmacogenomic information The Pharmacogenomic Knowledge Base 4 or PharmGKB designate 64 VIPs. PharmGKB - Pharmacogenomics Knowledge Base >PharmGKB.org Home at Stanford University PharmGKB collects, curates, and disseminates knowledge about the impact of human genetic variation on drug response. CPIC Guidelines Clinical Pharmacogenetics Implementation Consortium dosing, testing. 7

8 CYP P450 Enzymes CYP 2E1 <1% PGx CYP 2C9 15% CYP 3A4 50% Main Enzyme System for Drug Metabolism PGx CYP 2D6 25% PGx CYP 1A2 <1% CYP 2A6 <1% 2012 & 2017 FDA MedWatch Safety Alert FDA restricts use of prescription codeine pain and cough medicines in children; recommends against use in breastfeeding women Codeine contraindicated in children < 12 yrs. January 1969 to May 2015 FDA identified 64 cases of serious breathing problems, including 24 deaths in children younger than 18 years who received codeinecontaining medicines at usual doses. Why? Codeine Metabolism One of the first clinical application of PGx will be individualizing the dosing of specific drugs 200 X based affinity on for an individual s P450 enzyme activity (or lack mu thereof) receptor as determined by variation in the genes that code for these enzymes. Gene variants can result in slight differences in the protein structure produced (polymorphisms) that can render an enzyme non-functional, cause it to be produced in excess or not at all. Pharmacogenomic Application Genetic variations in the CYP enzymes of some people leads to differences in activity or amount of enzyme produced altering the rate or extent of metabolism Use permission granted PharmGKB 10 8

9 CYP2D6 Polymorphism Common polymorphisms or over 90 variants of this gene and enzyme exist, resulting in varying degrees of enzyme activity. Variation in the gene that encodes for CYP2D6 results in rapid, normal, reduced, or a complete lack of CYP2D6 function. The gene for CYP2D6 is located on Chromosome 22 remember you have two copies of the gene one from each parent. Single Nucleotide Polymorphism SNP snip A substitution of a nitrogenous base within a gene that changes the usual sequence. typo C T G G A A T C C C T G G G A T C C Glutamic Acid Glycine Copy Number Variation (CNV) Comparator -Reference Sequence or Wild Type Allele *1 Duplications or Multiplications CYP2D6 * 9 x N Allele Deletions CFTR F508 del or F508 9

10 CYP2D6 Gene Alleles PharmVar 1 CYP 2D6 Activity Level Examples of CYP2D6 Alleles No-Function (Null ) Alleles *3A *3xN *4 *4X2 *5 *6 *7 *8 *11 *12 *15 *18 *19 *20 *21 *31 *33 *35 *38 *42 *44 *56 *68 *69 Reduced Function Alleles *9 *10A, *10B *10X2 *41 *49 *50 *54 *55 *59 *69 *72 Normal Function Alleles *1A Wild Type *1B *1C *2A *27 *33 *35A Increased Function Alleles *1XN *2XN *35X2 *53 Unknown Many CYP2D6 Metabolizer Class-Codeine 5 Metabolizer Genotype Phenotype (Allele Combination) Ultrarapid (UM) Multiple copies >2 of normal or increased activity alleles (CNV gene duplication) or mutation in promoter region.*1/*1xn, *2xN/*1 Extensive (EM) At least one normal function allele *1/*1 Intermediate (IM) Two reduced function or one reduced and one no-function allele. *9/*41 or *9/*3A Poor (PM) Two no-function alleles *10/*17 Use alternative analgesics in CYP2D6 Ultrarapid and Poor Metabolizers. A label recommended age or weight specific codeine dose is warranted for CYP2D6 Extensive and Intermediate Metabolizers. 10

11 Genotype Directed Therapy for CF Cystic Fibrosis is caused by variations in the Transmembrane Conductance Regulator (CFTR) Gene which result in CFTR proteins that differ in structure and possess limited to no ability to transport chloride and other ions across exocrine cell membranes mainly in lung and pancreatic duct epithelium. 6 In one subset, CFTR gene variation is caused by the deletion of one phenylalanine amino acid. CFTR F508del Genotype Directed Therapy for CF ivacaftor, ivacaftor / lumacaftor CFTR Correctors and Potentiators - correct the malfunctioning protein by changing its conformation and help defective CFTR move to the cell s surface and open the gates. The FDA-approved drug label states that these drugs are only indicated for treatment of CF in patients > age 12 yrs. who are homozygous (two copies) for the F508del mutation in the CFTR gene. Predicting Risk of Toxicity 11

12 HLA Genes & Carbamazepine Toxicity Severe cutaneous hypersensitivity reactions are associated with the presence of specific HLA gene alleles. Stevens-Johnson Syndrome, SJS & Toxic Epidermal Necrolysis, TEN. Human Leukocyte Antigen (HLA-A, HLA-B) genes are part of a complex of genes that encode for cell surface proteins involved in presenting antigens to the immune system. Possessing one copy of the HLA-B*15:02 allele or the HLA-A*31:01 allele, places a person at higher risk for severe skin reactions. Ancestry & Carbamazepine Toxicity The HLA-B*15:02 variant is carried by: >15% of Hong Kong Chinese, Thailand, Malaysia, Philippines ~10% of Han Chinese ancestry ~2-4% of North Chinese, South Asians, Indian ancestry <1% of Japanese, Korean ancestry HLA-A*31:01 variant is carried by: >15% of Japanese, Native American, Southern Indian and some Arabic ancestry. ~10% of Han Chinese, Korean, European, Latin American, and other Indian ancestry. ~5% of African-Americans, Thai, Taiwanese, Hong Kong Chinese ancestry. FDA Table of Pharmacogenomic Biomarkers in Drug Labeling 7 Drug Link in Drugs@FDA Therapeutic Area HUGO Symbol Referenced Subgroup Label Sections with Pharmacogenomic Information Carbamazepine Neurology HLA-B Carbamazepine Neurology HLA-A HLA-B*1502 allele carriers HLA-A*3101 allele carriers Boxed Warning Warnings and Precautions Boxed Warning Warnings and Precautions 12

13 Package Insert Carbamazepine Boxed Warning Relaying Real Risk WARNINGS Serious Dermatologic Reactions Serious and sometimes fatal dermatologic reactions, including toxic epidermal necrolysis (TEN) and Stevens-Johnson syndrome (SJS), have been reported with Tegretol treatment. The risk of these events is estimated to be about 1 to 6 per 10,000 new users in countries with mainly Caucasian populations. However, the risk in some Asian countries is estimated to be about 10 times higher. Tegretol should be discontinued at the first sign of a rash, unless the rash is clearly not drug-related. If signs or symptoms suggest SJS/TEN, use of this drug should not be resumed and alternative therapy should be considered. FDA Recommended Action WARNINGS Prior to initiating Tegretol therapy, testing for HLA-B*15:02 should be performed in patients with ancestry in populations in which HLA-B*15:02 may be present. Laboratory Tests For genetically at-risk patients (see WARNINGS), high-resolution HLA-B*15:02 typing is recommended. The FDA-approved label for carbamazepine (Tegretol) states that a moderate association has been found between HLA-A*31:01 and the risk of developing hypersensitivity reactions to carbamazepine, but does not mandate testing. CPIC Guideline for Carbamazepine and HLA-A, HLA-B Recommends an alternative drug for CBZ-naive patients carrying at least one copy of either HLA- B*15:02 or HLA-A*31:01 due to the association of those alleles with an increased risk of Stevens- Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). In addition, HLA-A*31:01 is associated with an increased risk of drug reaction with eosinophilia and systemic symptoms (DRESS) and maculopapular exanthema (MPE). 13

14 Ad in Delta Sky Magazine 4/2017 Genetic Testing / Sequencing It is the reduction in the cost and the time it takes to sequence that has accelerated PGx translation $10 million > 2015 $1,400 Whole genome sequencing identifies all 3 billion base-pairs. Targeted sequencing identify the base sequence of genes of interest. Results are typically presented with annotation or interpretation & delivered to patients. The Time is Now! To embrace new advancements in medical science that improve the safety and efficacy of drug therapy. To stay updated with PharmGKB about new genedrug associations & FDA recommendations. To seek opportunities for Pharmacists to lead PGx translation into clinical practice & be compensated for our cognitive work! 14

15 Thank You! Speaker Contact Information: Kathleen B. Orrico PharmD,BCPS Phone: (650) References Citation 1 Gaedigk, A., Ingelman-Sundberg, M., Miller, N. A., Leeder, J. S., Whirl-Carrillo, M., Klein, T. E. and the PharmVar Steering Committee (2018), The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database. Clin. Pharmacol. Ther., 103: doi: /cpt.910 Citation 2 Genetics Home Reference. [Internet]. U.S. National Library of Medicine. Bethesda, MD. Help Me Understand Genetics. Available at: [updated 10/17/17; cited 02/20/18] Citation 3 National Institutes of Health National Human Genome Research Institute [Internet] Talking Glossary of Genetic Terms Available at: [cited 02/28/18] Citation 4 Whirl-Carrillo M, McDonagh EM, Hebert JM, et. al. Pharmacogenomics Knowledge for Personalized Medicine. Clin Pharmacol Ther. 2012; 92(4): doi: /clpt Available at: [cited 9/26/2017] Citation 5 Owen R, Sangkuhl K. Very Important Pharmacogene: CYP2D6 The Pharmacogenomic Knowledge Base [Internet] PharmGKB Available at [updated 02/14/09; cited 02/26/18] Citation 6 Ong T, Ramsey BW. New Therapeutic Approaches to Modulate and Correct CFTR. Pediatric clinics of North America. 2016;63(4): doi: /j.pcl Citation 7 FDA Table of Pharmacogenomic Biomarkers in Drug Labeling [updated 12/2017; cited 02/26/18] 15