Pharmacogenomics

Presented by: Narjes Khatoon Shabani SadrProvide for : Seminar of Human Genetics-

Dr.forughmand

) عج ) مهدی رب بسم

What is pharmacogenomics?

Pharmacogenomics is the study of how an individual's genetic inheritance affects the body's response to drugs.

The term ‘Pharmacogenomics’ comes from the words ‘pharmacology’ (the science of drugs) and ‘genomics’ (the study of genes and their functions) and is thus the intersection of pharmaceuticals and genetics.

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Shahid Chamran university of Ahvaz

personalized and Pharmacogenomics

• Pharmacogenetics- is often a study of the variations in a targeted gene, or group of functionally related genes.

• Pharmacogenomics , on the other hand is a much broader investigation of genetic variations at the level of the genome

Pharmacogenomics includes Pharmacogenetics

Factors involved in inter individual variation in drug response

INTRODUCTION TO PHARMACOGENOMICS

The goal of pharmacogenomics is to:

• understand polymorphisms of drug metabolizing enzymes

• transporters, and/or receptors that ultimately determine the outcome of drug therapy.



Differences in drug response in patients:• Genetic (genotype, gender, ethnic

background)• Environment (disease, previous

treatment and the environment)


Focus:At the beginning: On individual differencesBut Over time: Genetic differences between populations

pharmacogenomics is used For all organisms that are able to respond to drugs or other chemicals



Research in the field of pharmacogenetics is moving in two main directions:• 1) identify specific genes and their products that are

associated with different diseases and may be targets for new treatments.

• 2) Identification of genes and allelic variants of genes that may affect the response to drugs for diseases.

History of pharmacogenetics

First discovered of Pharmacogenetics was over 50 years ago.

A person with a genetic polymorphism leads to deficiency G6PD

The time needed to Treatment with primaquine

Hemolysis


• Pythagoras510 BC(Some people eat fava anemia)• Fredrich Vogel Word of pharmacogenetics(at first In 1959)• Sir Archibald Garrod The role of genetics in response to

drugs(1990)• In 1990, the emergence and development of the field was

divided into four periods:The first stage (1910-1850)The second stage (1950-1910) The third stage (1990-1950)The fourth stage (1990 and thereafter)


The first stage(1910-1850)With the discovery of three findings : The ability of the body's metabolism of foreign substances

(chemists and physiologists)

Mendelian inheritance (Gregory Mendel)

and drug receptors (Ehrlich)

Sir Archibald Garrod Said:Errors of metabolism and chromosome in human and therefore specific and personal biochemistry in each person is hereditary.

History of pharmacogeneticsThe second stage (1950-1910) it seems to me, the most important step

Archibald Garrod, William Bateson ,Lucien Cuenot genetic material has an important role in the transfer of chemicals and chemical changes.

Marshal(1918) Blacks are more than resistant whites, against the mustard gas

Chen & middleton Changes of ephedrine, and cocaine in the expansion of eyes in white, black and Chinese are different.

1920s Differences in perceptions and emotions were discovered. Synder(1932) Deficiency of taste is an inherited

Alcohol dehydrogenase and aldehyde dehydrogenase deficiency Was discovered.

History of pharmacogenetics N- acetyltransferase polymorphism Racial distribution and depends on

the latitude of countries. Finally, double-stranded helix structure of DNA was discovered.

Polymorphism discovery in hemoglobin Sickle cell disease the SNP of: HFE gene hemochromatosis Apolipoprotein E=ApoE Cardiovascular and Alzheimer's disease, Factor’s gene 5 and protrombin gene thrombosis Methylene Tetra Hydro Folate Reductase=MTHFR) Venous

thromboembolism

Start correct and systematic pharmacogenetics.

thus


The third stage (1990-1950) and The fourth stage (1990 and thereafter)

• In 1956 the human chromosomes were observed.• Chronic myelogenous Leukemia(CML) Its association with chromosomal

defects (Philadelphia chromosome)• Advances in technology• The inheritance pattern of responses to some of the drugs were found

during this period.

• Until 1990, about100 of properties polymorphic and monomorphic pharmacogenetics were identified.

There is a great deal of variability at the DNA level between individuals that governs many characteristics of the person, including his or her ability to respond to a particular drug therapy:SNPs account for over 90% of the genetic variations

in the human genome. deletions, tandem repeats, and microsatellites

Genetics and metabolism of drugs

Single-nucleotide polymorphisms(SNPs) effect on Pharmacogenomics :

Single Nucleotide Polymorphism (SNP):

GAATTTAAG

GAATTCAAG

SNPs are defined as Single base-pair positions in genomic DNA that vary among individuals in one or several populations.

SNPs are believed to underlie susceptibility to such common diseases as cancer, diabetes, and heart disease and to contribute to the traits that make individuals unique.

SNPs are used as genomic biomarkers.

Hence SNP analysis can be used to enhance drug discovery and development.DNA molecule 1 differs from

DNA molecule 2 at a single base-pair location (a C/T polymorphism) Shahid Chamran university of Ahvaz

Clinical trials and the creation of an SNP linkage disequilibrium database for a

fictitious drug



Based on the response to a drug, individuals can be classified as poor or extensive metabolizers.

Molecular genetic testing can characterize an enzyme’s gene to demonstrate which alleles (genetic polymorphisms) are present, and how such alleles may affect enzymatic activity.

Some of these alleles may be associated with loss or reduction of gene function (alleles are denoted by an asterisk (*) and a number). In general, *1 usually means a normally functioning gene, and hence a normally functioning enzyme.

Different metabolizers of a drug that depend on genetic makeup include:

Extensive Metabolizers (EM): Individuals who have two normal genes metabolize a drug normally.

Poor Metabolizers (PM): Individuals with two non-functional

genes metabolize a drug very slowly compared to a normal individual (EM).

Ultra-Rapid Metabolizers (UM): These individuals may have

multiple copies of active genes and may metabolize a particular drug so fast that the drug doesn’t have any

pharmacological effect.

Intermediate Metabolizers (IM): These individuals may have

one active and one non-active allele for the same gene.

Enzymes involved in drug metabolism



Drug target

There are three types of genetic variety:

Some cases which play a role in the transmission, distribution and elimination of external factors.

Those that cause adverse drug reactions in the body.

And genetic variation which are targets of a drug.

DRUGTARGETS

DRUGMETABOLIZING

ENZYMES

DRUGTRANSPORTERS

PHARMACOKINETICSPHARMACODYNAMICS

Variability in Efficacy/Toxicity

Drug target

Genetic variants in response to therapeutic agents:

Enzymes which play a role in drug metabolism

A drug targets proteins (transmitter and receiver drug or drug carriers).

POLYMORPHISM OF ENZYMES RESPONSIBLE FOR DRUG METABOLISM

Most drugs undergo phase I metabolism, which involves oxidation, reduction, or hydrolysis. Such reactions transform the drug into a more polar water-soluble metabolite.

some drugs can undergo phase II metabolism, which entails conjugation of a polar group to the drug molecule to make it more polar.

Enzymes responsible for such transformations may show a wide variation in enzymatic activities due to genetic polymorphisms.

The goal of pharmacogenomics is to understand such genetic variations in order to predict the response of a particular drug in a particular patient.

POLYMORPHISM OF ENZYMES RESPONSIBLE FOR DRUG METABOLISM

The cytochrome P-450 mixed-function oxidase (CYP)

are N-acetyltransferase (NAT1 and NAT2)

thiopurine-S-methyltransferase (TPMT)

polymorphism of uridine-5 diphosphate glucuronyl transferase (UDP-glucuronyl transferase)

Effect of Cytochrome P450 Enzymes on Drug Metabolism:

The cytochrome P-450 mixed-function oxidase (CYP), the most important family of enzymes responsible for drug metabolism, comprises a large group of heme-containing enzymes.

These enzymes are found in abundance in the liver and other organs.

The major CYP isoforms responsible for the metabolism of drugs include CYP1A2, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP2E1, and CYP3A4/CYP3A5.

Effect of Cytochrome P450 Enzymes on Drug Metabolism:

Cytochrome P450 enzymes are essential for the metabolism of many medications.

The most significant enzymes are : CYP3A4 and CYP2D6.


Enzymes involved in Pharmacogenomics:

Cytochrome P450 (CYP) family of enzymes is involved in metabolism of several drugs.

Example: CYP2D6 enzyme

CYP3A4 enzyme CYP2A6enzyme CYP2B6 enzyme CYP2C9enzyme CYP2C19enzyme CYP2E1 enzyme

An example of different CYP2D6 alleles and their effects on enzyme function

Key points regarding CYP enzymes:

CYP3A4 is the predominant isoform of the CYP family (almost 30%), and is responsible for the metabolism of many drugs.

Genetic polymorphisms of CYP2D6, CYP2C9, and

CYP2C19 have been well studied and account for some wide interindividual responses to various drugs. If the enzymatic activity is lost or significantly reduced due to a genetic polymorphism, then the individual may not be able to metabolize a particular drug (that is typically metabolized through that enzyme) effectively, and can suffer from drug toxicity.

Other polymorphically expressed drug-metabolizing enzymes

a polymorphism of uridine-5 diphosphate glucuronyl transferase (UDP-glucuronyl transferase) may also play a vital role in metabolism of certain drugs (e.g. irinotecan, an anticancer drug).

This enzyme is responsible for conjugation of glucuronic acid with the drug molecule in phase II metabolism, thus inactivating the drug.

This enzyme is mostly found in the liver, but may also be present in other organs.

There are two main families of UDP-glucuronyl transferase: UGT1 and UGT2.

Polymorphisms of UGT1A1 and UGT2B7 play important roles in the phase II metabolism of certain drugs.

Other polymorphically expressed drug-metabolizing enzymes

N-acetyltransferase (NAT1 and NAT2) and thiopurine-S-methyltransferase (TPMT).

The slow acetylator phenotype of the NAT1/2 polymorphism results in isoniazid-induced peripheral neuropathy and sulfonamide-induced hypersensitivity reactions

while TPMT catalyzes inactivation of various anticancer and anti-inflammatory drugs.

Polymorphisms of the transporter and receptor proteins:

Most drug responses Interaction of several gene products that affect the pharmacokinetics and pharmacodynamics.

Today 500 to 1200 genes of drug transporter have been identified

The best example of a drug transporter: multidrug-resistant transporter and p-glycol- protine /MDR1

AmpliChip CYP450Using FDA-approved test kit

• Determine the genotype of the patient in terms of two CYPP450 enzymes: 2D6 and 2C19

• FDA approved the test on December 24, 2004. The AmpliChip CYP450 test is the first FDA approved pharmacogenetic test.

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Pharmacogenetics testing methods

Technologies and methods that used in pharmacogenetics:

1. The DNA microarray

2- pyro-sequencing

3. Mass Spectrometry

4-Fluorescence based-platform

5-RFLP and RTPCR and their types (such as PCR-5 QPCR)

Pharmacogenetics and clinical application

pharmacogenomics is one of the main members of Individual therapy.

Recipients of treatment with:o Warfarino Chemotherapy by Specific anticancer drugso Pain management with certain opioids

Examples of drugs where pharmacogenomics testing is useful are listed in this Table



Pharmacogenetics in oncology:Pharmacogenetics focused on the effects of genetics in cancer treatment.

Pharmacogenetics And selection of anticancer drugs:• Thiopurine• Irinotecan،• Tamoxifen

Thiopurine such as : 6-mercaptopurine (6-MP) thioguanine and azathioprine (TPMT)

Metabolized by: thiopurine-S-methyl transferase (TPMT)


Metabolism of 6-mercaptopurin to 6-methylmercaptopurin by the methylator TPMT.

Various alleles of the gene TPMT and their SNPs.

The metabolic pathway of azathioprine

Irinotecan

Irinotecan

7-ethyl-10- hydroxycamptothecin (SN-38)

(UGT1A1) UDP- glucuronosyl transferase

Active metabolite

Detoxification

Irinotecan

Tamoxifen (estrogen receptor-positive breast cancer)

Tamoxifen is a prodrug

endoxifen (4-hydroxy-N-desmethyl-tomoxifer)

Tamoxifen

By CYP2D6

Pharmacogenetics in Cardiovascular Disease


• Current Status of Pharmacogenetics in Antithrombotic Drug Therapy:

• The impact of VKORC1 and CYP2C9 variants on warfarin response, established the value of genetic variability to predict the appropriate warfarin dose for improving and easing the transition to a therapeutic INR level.


Pharmacogenetics and warfarin treatment

• Respond differently to warfarin dose: CYP2C9 genetic polymorphisms Vitamin K epoxide reductase complex (VKORC1)

Patients with CYP2C9 * 2 and CYP2C9 * 3 alleles Need lower maintenance dose of warfarin

Warfarin consists of a racemic mixture of two active enantiomers—R and S- forms


Antiplatelet drug Clopidogrel


Drugs used for pain management, such as:

Codeine , Dihydrocodeine, Fentanyl ,Hydrocodone Methadone ,Morphine ,Oxycodone ,Tramadol, Tricyclic antidepressante

• Metabolized By :

• polymorphic CYP450 enzymes such as:CYP2D6 and CYP3A4

• And UGT2B7(uridine diphosphate glucuronyl transferase 2B7)

Pharmacogenetics in Selection of opioids


• ultra-metabolizers Multiple copies of the gene CYP2D6

• extensive-metabolizer With a single copy of the wild type gene of CYP2D6

• intermediate metabolizers Decrease in enzyme activity

• poor metabolizers any activity

The metabolic pathway of codeine in the body

The metabolism of codeine to morphine by CYP2D6


The tricyclic antidepressant amitriptyline is metabolized by CYP2C19 to the active metabolite nortriptyline.

CYP2D6 is needed for deactivation of nortriptyline.

Adverse drug reactions tend to be associated with nortriptyline concentrations,

And poor metabolizers of CYP2D6 are more likely to suffer from adverse effects due to the build-up of nortriptyline concentrations.

Pharmacogenetics in Selection Psychoactive drugs

Pharmacogenetics in other miscellaneous drugs

• Organ transplant recipients receive immunosuppressants in order to prevent organ rejection.

• These drugs are metabolized by the cytochrome P-450 family of enzymes, including CYP3A4 and CYP3A5.

• Although polymorphisms of CYP3A4 do not alter the enzyme activity significantly,

• polymorphisms of CYP3A5 may be clinically more significant because enzyme activities can vary significantly between different alleles.

Pharmacogenetics in other miscellaneous drugs

• Pharmacogenomics testing can be used to identify polymorphisms of CYP3A5 to predict optimal initial dosage of Tacrolimus.

• HLA-B*1502, which is more abundant among Asians, is associated with severe skin rashes (including Stevens Johnson syndrome) following treatment with carbamazepine.

• HLA-B*5701 is strongly associated with hypersensitivity towards the anti-HIV drug abacavir.

• HLA-B*5801 is associated with hypersensitivity to allopurinol


1. Preparing profiles related to sensitivity of the pharmaceutical, food and other external factors.

2. Preparing profiles of the SNP.

3. Create profiles of diagnostic markers and laboratory tests

4. Determination of the location of the cell and function of proteins and metabolic pathways in different cell lines.

Necessary action to Advancement of pharmacogenetics in the future


5. Preparing profiles of ethnic diversity and racial.

6. The appropriate design of drugs

7. Comparison profiles between the genomes of different organisms

Necessary action to Advancement of pharmacogenetics in the future

Challenges in pharmacogenetics

Necessary conditions for stratified medicine.

Therapeutic continuum: empirical, stratified, and personalized medicines

Pharmacogenetic tests validated in clinical studies and recommended in the drug labels are detailed in table 1.

Irinotecan CAMPTOSAR®

CRC UGT1A1

First FDA approved pharmacogenetic test ““Third Wave Technologies, Invader assay”” (2005), with dose optimization guidelines dependent on UGT1A1 genotype: avoid severe (grade III/IV) neutropenia and diarrhoea for those who are at high risk, i.e. Homozygous (and possibly heterozygous) for UGT1A1*28 and UGT1A1*1 alleles.

Warfarin COUMADIN®

Thrombo-embolism

CYP2C9 and VKORC1 (-1639G>A)

Improve drug efficacy and safety: avoid increased risk of bleeding to patients homozygous or heterozygous for CYP2C9*2 or CYP2C9*3 alleles by prescribing differentiated doses (as compared with those for CYP2C9*1 homozygous). Pharmacogenetic test: ““Nanosphere Verigene Warfarin Metabolism Nucleic Acid Test; therapeutic algorithm based on genotype and clinical factors (http://www.WarfarinDosing.org.)

Clopidogrel (prodrug) PLAVIX®

Thrombo-embolism CYP2C19

Improve efficacy and safety: doses adjustment for ultrarapid metabolizers who are carriers of CYP2C19*17/*17 genotype and for poor metabolizers due to CYP2C19*2 allele presence.

Carbamazepine TEGRETOL®

Epilepsy

HLA-B*1502 allele

Improve drug safety: avoid serious dermatologic reactions (Stevens––Johnson syndrome and/or toxic epidermal necrolysis).

Drug Indication

Pharmacogenetic biomarker Comments

Rasburicase ELITEK®

Hyperuricemia G6PD

Improve drug safety: pre-therapy screening to avoid severe hemolytic reactions associated with G6PD deficiency.

Clozapine CLOZARIL®

Schizophrenia HLA-DQB1

Improved safety: pharmacogenetic testing, in parallel with WBC monitoring, avoid prescription to patients with high agranulocytosis risk. Test „„PGxPredict: Clozapine””

Tretinoin VESANOID® APL PML/RARD Improve drug efficacy and safety.

Disease confirmation by t(15;17) cytogenetic marker

Valproic acid DEPAKENE®

Seizures UCD deficiency

Confirm disease: consider evaluation of UCD before therapy with valproate

Only informational pharmacogenetic tests in drug label Panitumumab VECTIBIX®

Cetuximab ERBITUX®

mCRC K-RAS Improve efficacy: clinical benefit limited to patients with nonmutated K-RAS.

Imatinib GLEEVEC®

GIST C-KIT

Improve drug efficacy: clinical benefit in patients carriers of the activating C-KIT mutation

Busulfan MYLERAN®

CML

Philadelphia chromosome

Improve drug efficacy: responders are positives for Philadelphia chromosome (BCR-ABL)

Capecitabine XELODA®

CRC DPD deficiency

Improve drug safety: decreased DPD and increased level of 5fluorouracil is associated with severe toxicity (e.g., stomatitis, diarrhoea, neutropenia and neurotoxicity).

Primaquine Malaria G6PD deficiency

Improve drug safety: avoid acute intravascular hemolytic reactions.

Isoniazid, Pyrazinamide TB NAT

Improve drug safety: dose adjustements based on NATmetabolic status, for slow acetylators and fast acetylators to avoid severe adverse reaction of peripheral neuropathy, or lack of efficacy, respectively.

Erlotinib TARCEVA®

NSCLC EGFR mutations Confirm disease (at least 10% of the cells are EGFR-positive) and response to EGFR tyrosine kinase inhibitors

Lenalidomide REVLIMID®

Myelodysplasic syndromes

Deletion of chromosome 5q (del[5q])

Confirm disease: indicated to treat those with transfusion dependent anemia caused by low- or intermediate-risk of myelodysplasic syndromes associated with 5q(del[5q])

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Sha

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cham

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univ

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Department of Genetics, Harvard University

Genetics is not perceived simply as a subject, but rather as a way of viewing and approaching biological

phenomena.

Health & Medicine

Pharmacogenomics