Pharmacogenomics: an overview

Dr. dr. Mgs. Irsan Saleh, M.Biomed

Dept of Pharmacology Faculty of Medicine Sriwijaya University

irsan_saleh_hasani@yahoo.com

Disease Drug Class Rate response (%)

Asthma β-agonists, others 25-60

Solid cancer various 0-30

Depression SSRIs, tryciclic, others 60-80

Diabetes Sulfonylurea, others 25-50

Arthritis NSAIDs, COX-2 inhibitors, others

50-80

Migraine Triptan, NSAIDs, ergot 40-70

Schizoprenia Various 25-75

Major drug toxicity

Various 2 million hospitalized patients/y, 4th-6th leading

cause of death in US 1994

Interindividual variability in drug response

• AgeAge• EnvironmentalEnvironmental• WeightWeight• GenderGender• Concomitant DiseasesConcomitant Diseases• Concomitant DrugsConcomitant Drugs• Social factorsSocial factors• GeneticsGenetics

Factors contributing to interindividual variability in drug response

Pharmacon

Pharmacogenomics

Genome

The study of genome-derived data, including human genetic variation, RNA and protein expression differences, to predict

drug response in individual patients or groups of patients.

The entire DNA content of a cell, including all of genes

and all of the intergenic regions.

The chemical substance that influence biological function

at molecular, cell or organs of organism.

Definition

• The application of genome science (genomics) to the study of human variability in drug response.

• The study of genetic content (DNA sequence) of humans for drug discovery & optimization.

• Refer to the general study of all many different genes that determine drug behavior.

Other definition

1. Vision and some predictive observations

History

• Garrod (1902) : alcaptonuria and phenylketonuria due to biochemical individuality.

• Snyder (1932) : a heritable disability to taste phenylthiocarbamide.

• Savin & Glick (1943) : a genetic lack atropine esterase in some rabbits.

History (cont. …)

2. Pharmacogenetics lives: systemic case studies

• 1950 : several observation indicated clearly the dependence drug effects on the genetic constitution.

• Variation in isoniazid acetylation

• Variation in cholinesterase activity

• Hemolysis cused deficiency G-6-PD

• Motulsky (1957) : Drug reaction, enzymes and biochemical genetics

• Vogel (1959) : coined the Pharmacogenetics

• Kalow (1962) : summarized all available knowledge in a book

History (cont. …)

• Manya centers contributed new data, but data represented monogenic variations.

• Weber’s book (1997) : listed 15 variable metabolizing enzymes, 11 variable drug receptors, 14 other variable

• Kalow (2001) : counted 42 variable drug-metabolizing enzymes

• The enzyme’s variation are complex: mutations, spicing defects, gene deletion, present or stop codon.

• Many clinical case study due to enzyme’s variation reported and genetic failure of drug-metabolizing enzyme’s can lead to a patient’s death.

3. Broadening of pharmacogenetic knowledge

4. Pharmacogenetic differences between population

History (cont. …)

• Paskind (1921): atropine sulfat caused a initial slowing of heart rate in Caucasian (20) but not African-American subjects.

• Chen & Poth (1929): variation in pupillary size after applying mydriatic eye drop (increase largest in Caucasian, intermediate in Asians and smallest in African American).

• Sunahara et al. (1961): Genetical and geographical studies in isoniazid inactivation.

• Beutler (1993): primaquine caused hemolysis on African soldiers due to deficiency G6PD

• Kalow (2001): 11 mutations of CYP2D6 was tested : European carried 7, Chinese 4, Japanese 3 and Africans 2.

History (cont. …)

• Differences between people in their response to drugs are regular occurrences.

• The causes of most differences generally remain uninvestigated, but the presence of both genetic and environmental cause is common.

• It is of considerable interest to know the relative contribution of the two causes.

• Kalow et al. (1999; 1998) : assess the genetic component in pharmacological variability

5. The rise of multifactorial pharmacogenetics

The proportion of the disease that is due to genetic factors

0% 50% 100%

HDL level

RheumatoidArthritis

Schizophrenia

Huntington'sDisease

GenesEnvironment

History (cont. …)

History (cont. …)

6. Advances in molecular biology

1967 Gilbert discovered DNA ligase1972-73 DNA cloning techniques established by

Boyer, Cohen and Berg1988 The first biothechnology products appear.

These were tissue plaminogen factor, α-interferon, human insulin, human growth factors and erythropoetin.

1990 Human genome project was initiated and finished at 2003

Drug respons

DietEnvironment

Lifestyle State of health

Genetics

Pharmacogenetics

Drug Metabolism

Drug Effects

• Slow & rapid acetylation of INH • Poor & large hydroxylation of Debrisoaquin

• Deficiency of G-6-P dehidrogenasi sulfonamide• High activity cholinesterase succinylcholine

Pharmacogenetics : • the use of genetic content of humans to understand drug effects. • refer to the study of inherited difference (variation) in drug metabolism & response

Pharmacogenomics : • the use of genetic content (DNA sequence) of humans for drug discovery & optimization• refer to the general study of all many different genes that determine drug behavior

7. Pharmacogenomics and Pharamacogenetics

Drug discovery and development in genomics era

DNA Genomics

mRNA Transcriptomics

Protein Proteomics

Protein-complex Functional Proteomics

Metabolites Metabolomics

Cell level

Tissue level

Organ level

Fluids

High-throughput technologies

Robotics & Bioinformatics

System Biology

• Drug discovery & development • Identification & validation of new drug targets• Modeling of disease progression• Identification of novel diagnostic or prognostic markers• Pathogenesis of diseases

Pharmacogenomics ►

Drug respons

PharmacogenomicsPharmacogenomics

DRUGTARGETS

DRUGMETABOLIZING

ENZYMES

DRUGTRANSPORTERS

PHARMACOKINETICSPHARMACODYNAMICS

Variability in Efficacy/Toxicity

Johnson JA. Trends in Genetics 2003: 660-666

Drug Transporter

1. Drug transporters such as ABCB1, ABCC1, ABCC2, ABCC3 participate in opioid transport and influence opioid efficacy and side effects.

2. Substrates of ABCB1/MDR1 include morphine, methadone, fentanyl, sufentanil, alfentanil, and morphine-6-glucuronide and anticancer

3. Other transporters potentially involved in opioid distribution are MRP1, MRP2, and MRP3 (ABC transporter subfamily C), organic anion transporters (OAT1 and 3), and organic anion transporter polypeptides (OATP1 and 2, solute carrier family 21).

Drug Transporter (cont. …)

Drug Metabolizing EnzymesDrug Metabolizing Enzymes

Examples of Drug Metabolism PharmacogenomicsExamples of Drug Metabolism Pharmacogenomics

NEJM 2003; 348: 529-537

Examples of Drug Metabolism Pharmacogenomics Examples of Drug Metabolism Pharmacogenomics

NEJM 2003; 348: 529-537

Nortriptyline kinetics and CYP2D6 genotype(Dalén et al 1998)

Nortriptyline 10-OH-nortriptyline

CYP2D6

Examples of Drug Target PharmacogenomicsExamples of Drug Target Pharmacogenomics

Evans WE. NEJM 2003; 348:538-48

Beta-blockers and Beta-blockers and Hypertension (HTN)Hypertension (HTN)

• HTN is the most prevalent chronic disease in the HTN is the most prevalent chronic disease in the US and a contributor to morbidity and mortalityUS and a contributor to morbidity and mortality

• Beta-blockers are first-line agent in the Beta-blockers are first-line agent in the treatment of HTNtreatment of HTN

• Marked variability in response to beta-blockers Marked variability in response to beta-blockers – 30-60% of patients fail to achieve adequate blood 30-60% of patients fail to achieve adequate blood

pressure lowering with beta-blockerspressure lowering with beta-blockers

• Common beta-blockers used in HTN: Common beta-blockers used in HTN: – Metoprolol Metoprolol – AtenololAtenolol

Podlowski, et al. J Mol Med 2000;78:90.

Beta-1 Adrenergic ReceptorBeta-1 Adrenergic Receptor

Codon 49 SerGly

Codon 389ArgGly

Beta-1 Receptor Polymorphisms and Response Beta-1 Receptor Polymorphisms and Response to Metoprololto Metoprolol

Johnson JA et al. Clin Pharmacol Ther 2003; 74:44-52

Beta-2 Adrenergic Receptor Polymorphisms Beta-2 Adrenergic Receptor Polymorphisms and Response to Albuterol in Asthmaand Response to Albuterol in Asthma

• Hyperreactivity of the airways is the hallmark of Hyperreactivity of the airways is the hallmark of asthmaasthma

• Airway smooth muscle contains beta-2 receptors Airway smooth muscle contains beta-2 receptors that produce broncodilationthat produce broncodilation

• Albuterol is a beta-2 agonist that is used in the Albuterol is a beta-2 agonist that is used in the treatment of asthmatreatment of asthma– Produces smooth muscle cell relaxation and Produces smooth muscle cell relaxation and

bronchodilationbronchodilation

• Forced expiratory volume in 1 second (FEVForced expiratory volume in 1 second (FEV11))– Phenotypic measure of responsePhenotypic measure of response

Beta-2 Polymorphisms and Beta-2 Polymorphisms and Response to AlbuterolResponse to Albuterol

Lima JJ. Clin Pharmacol Ther 1999; 65:519-25

•Single 8 mg albuterol dose

•Albuterol-evoked increases in FEV1 were higher and more rapid in Arg16 homozyotes compared with Gly carriers

• Codon 16 polymorphism is a determinant of bronchodilator response to albuterol

Lima JJ et al. Clin Pharmacol Ther 1999; 65: 519-25

O

CH2

CH2

N CH3

OHCH3O

O

CH2

CH2

N CH3

OHHO

O

CH2

CH2

N CH3

OHGlukuronate O

CH2

CH2

N CH3

GlucuronateOH

O

CH2

CH2

N CH3

GlucuronateCH3O

Codein Pharmacogentics

Codein

Codein-6-glucuronate

Morphine-3-glucuronate Morphine-6-glucuronate

Morphine

CYP2D6• Ultrarapid Ultrarapid metabolizers (UMs)metabolizers (UMs)• Extensive Extensive metabolizers (EMs)metabolizers (EMs)• Poor metabolizers Poor metabolizers (PMs)(PMs)

Opioid receptor in brain

Drug transporter

Genetics polymorphism

Appling pharmacogenomics in drug discovery and development

IdeaIdea Marketed DrugMarketed Drug

YearsYears

11-15 Years11-15 Years

DiscoveryDiscovery Exploratory DevelopmentExploratory Development Full DevelopmentFull Development

Phase I Phase II Phase III

00 151555 1010

Phase IV

Disease genetics

Target variability

Selecting responsders

Pharmacogenetics

Choosing the best targets

Better understanding of our Targets

Improving early decision

making

Predicting efficacy and

safety

Choosing the best targets & better understanding targets

Drug discovery and development in genomics era

DNA Genomics

mRNA Transcriptomics

Protein Proteomics

Protein-complex Functional Proteomics

Metabolites Metabolomics

Cell level

Tissue level

Organ level

Fluids

High-throughput technologies

Robotics & Bioinformatics

System Biology

• Drug discovery & development • Identification & validation of new drug targets• Modeling of disease progression• Identification of novel diagnostic or prognostic markers• Pathogenesis of diseases

Pharmacogenomics ►

Drug respons

Identify disease

Isolate proteininvolved in disease (2-5 years)

Find a drug effectiveagainst disease protein(2-5 years)

Preclinical testing(1-3 years)

Formulation

Human clinical trials(2-10 years)

Scale-up

FDA approval(2-3 years)

File

IN

D

File

NDA

Choosing the best targets

GENETICSPHYSIOPATHOLOGY(in vitro, in vivo, ..)

FUNCTIONAL VALIDATION

• AS DRUGS• AS TARGETS

DRUGDISCOVERY

ANTIBODY DRUGS

RATIONAL DRUGDESIGN

HIGH THROUGHPUT SCREENING

PROTEINS DRUGS

(cf. EPO, Interferons, …)

STRUCTURE-BASED DRUG DESIGN(incl. in silico…)

- RELEVANT ASSAYS…- VERY LARGE LIBRARIES OF COMPOUNDS(SYNTHETIC OR NATURAL)

“INVENTORY”

DNA

Protein

SMALL MOLECULES DRUGS

DrugsGenomics

Proteomics

Improving early decision making

• Phase I studies

– Explain outliers or patient-to-patient variability in PK

– Exclude or include specific patients– Normalize genotype frequencies– Bridge to other populations

tt 1/2

1/2,

hr

, h

r

1010

2020

3030

4040

5050

Example: Desipramine PK Parameters

CYP2D6 *6/*9CYP2D6 *6/*9

Genotyping can increase trial safety and explain outlying dataGenotyping can increase trial safety and explain outlying data

Drug interaction studyDrug interaction study

• CYP2D6 poor metabolizers CYP2D6 poor metabolizers (2 null alleles) excluded.(2 null alleles) excluded.

• One outlier with slow One outlier with slow metabolismmetabolism

• Outlier has *6 null allele and *9 Outlier has *6 null allele and *9 allele with reduced enzymatic allele with reduced enzymatic activity. activity.

• Expected occurrence of null/*9 Expected occurrence of null/*9 genotype is 0.4%genotype is 0.4%

Katz et al., Abbott Labs.Katz et al., Abbott Labs.

• Phase II/III studies

– Identify genetically-defined groups with more pronounced or rapidly progressing disease

– Exclude/include at-risk individuals– Stratify studies based on genotypes

• Clinical response• Risk of adverse events

– Where appropriate, develop drugs for specific groups

– Identify genetic markers associated with clinical outcomes