Pharmacogenomics: The Promise of Personalized Medicine

1
PharmacogenomicsThe Promise of Personalized
Medicine

• Christina Aquilante, Pharm.D.
• Assistant Professor
• Department of Pharmaceutical Sciences
• School of Pharmacy
• University of Colorado at Denver and Health
  Sciences Center

2
Objectives

• Provide an overview of pharmacogenomics and its
  clinical relevance
• Discuss clinically-relevant examples of
• Drug metabolism pharmacogenomics
• Drug target pharmacogenomics
• Discuss the challenges facing pharmacogenomic
  studies and the movement of pharmacogenomics into
  clinical practice
• Discuss pharmacogenomics from the FDA and
  pharmaceutical industry perspective

3
Interindividual Variability in Drug Response

• Disease Drug Class Rate of Poor Response
• Asthma Beta-agonists 40-75
• Hypertension Various 30
• Solid Cancers Various 70
• Depression SSRIs, tricyclics 20-40
• Diabetes Sulfonylureas, others 50
• Arthritis NSAIDs, COX-2 inhibitors 30-60
• Schizophrenia Various 25-75

4
Factors Contributing to Interindividual
Variability in Drug Disposition and Action

• Age
• Race/ethnicity
• Weight
• Gender
• Concomitant Diseases
• Concomitant Drugs
• Social factors
• GENETICS

PERSONALIZED MEDICINE
5
We wish to suggest a structure for the salt of
DNA. This structure has novel features which
are of considerable biological interest.
6
Human Genome Project

• Determine the sequence of the 3 billion
  nucleotides that make up human DNA
• Characterize variability in the genome
• Identify all the genes in human DNA
• The Era of Genomic Medicine
• Improve prediction of drug efficacy or toxicity
• Improve the diagnosis of disease
• Earlier detection of genetic predisposition to
  disease

7
Newsweek June 25, 2001
pharmacogenetics promises to target treatment
to a patients genetic profile
8
Genetics or Genomics?

• Pharmacogenetics
• Study of how genetic differences in a SINGLE gene
  influence variability in drug response (i.e.,
  efficacy and toxicity)
• Pharmacogenomics
• Study of how genetic (genome) differences in
  MULTIPLE genes influence variability in drug
  response (i.e., efficacy and toxicity)

9
Current Concept of Pharmacogenomics
Roden DM et al. Ann Intern Med 2006 145749-57
10
Potential of Pharmacogenomics
11
Clinical Relevance

• Can we predict who will derive an optimal
  response?
• Can we predict who will have a toxicity?
• Host (patient) genotype determines optimal drug
  therapy approach
• Disease (pathogen) genotype determines optimal
  drug therapy approach

12
DNA is Information

• DNA
• A, T, G, C
• Codon
• Gene
• Chromosome
• Genome

• ENGLISH
• Abcdefg.xyz
• Word
• Sentence
• Chapter
• Book

13
Composition of the Human Genome

• Mutation/Polymorphism 1 bp
• Unit of genetic code 3 bp
• Coding sequence (exons) 3,000 bp
• Gene (exons and introns) 50,000 bp
• Chromosome 150,000,000 bp
• Human genome 3,000,000,000 bp

14
The Foundation of Pharmacogenomics Differences
in the Genetic Code Between People

• Mutation difference in the DNA code that occurs
  in less than 1 of population
• Often associated with rare diseases
• Cystic fibrosis, sickle cell anemia, Huntingtons
  disease
• Polymorphism difference in the DNA code that
  occurs in more than 1 of the population
• A single polymorphism is less likely to be the
  main cause of a disease
• Polymorphisms often have no visible clinical
  impact

15
Single Nucleotide Polymorphisms (SNP)

• Pronounced snip
• Single base pair difference in the DNA sequence
• Over 2 million SNPs in the human genome
• Other polymorphisms
• Insertion/deletion polymorphisms
• Gene duplications
• Gene deletions

16
(No Transcript)
17
Consequences of Polymorphisms

• May result in a different amino acid or stop
  codon
• May result in a change in protein function or
  quantity
• May alter stability of mRNA
• No consequence

18
Genetics Terminology

• Alleles different DNA sequences at a locus
• Codon 389 ?1-AR
• Arg (0.75)
• Gly (0.25)

• Genotype pair of alleles a person has at a
  region of the chromosome
• Codon 389 ?1-AR
• Arg389Arg
• Arg389Gly
• Gly389Gly

19
Genetics Terminology

• Phenotype outward manifestation of a trait
• Linkage measure of proximity of 2 or more
  polymorphisms on a single chromosome
• Polymorphisms in close proximity tend to be
  co-inherited
• Regions of linked polymorphisms are known as
  haplotypes

20
Haplotype Map

• For specific locations in the genome, a small
  number of SNP patterns (haplotypes) can account
  for 80-90 of entire human population
• International HapMap Project
• Identifying common haplotypes in four populations
  from different parts of the world
• Identifying tag SNPs that uniquely identify
  these haplotypes

21
Pharmacogenomics
DRUG TARGETS
DRUG METABOLIZING ENZYMES
DRUG TRANSPORTERS
PHARMACOKINETICS
PHARMACODYNAMICS
Variability in Efficacy/Toxicity
Johnson JA. Trends in Genetics 2003 660-666
22
Drug Metabolism Pharmacogenomics

• Evidence of an inherited basis for drug response
  dates back in the literature to the 1950s
• Succinylcholine 1 in 3000 patients developed
  prolonged muscle relaxation
• Monogenic
• Phenotype to genotype approach

23
Drug Metabolizing Enzymes
24
Examples of Drug Metabolism Pharmacogenomics
NEJM 2003 348 529-537
25
Examples of Drug Metabolism Pharmacogenomics
NEJM 2003 348 529-537
26
Warfarin and CYP2C9

• Widely prescribed anticoagulant drug used to
  prevent blood clots
• Narrow range between efficacy and toxicity
• Large variability in the dose required to achieve
  therapeutic anticoagulation
• Doses vary 10-fold between people
• CYP2C9 is the enzyme responsible for the
  metabolism of warfarin
• SNPs exist in CYP2C9 gene that decrease the
  activity of the CYP2C9 metabolizing enzyme

27
CYP2C9 Polymorphisms and Warfarin Dose

• Warfarin dose is affected by CYP2C9 genotype

2 and 3 are SNPs
Gage BF et al. Thromb Haemost 2004 91 87-94
28
CYP2C9 Genotype and Bleeding Events

• Compared to wild-type, CYP2C9 variants had a
  higher risk of serious or life-threatening bleeds
• Hazard Ratio of 3.94 during the first 3 months of
  follow-up
• Hazard Ratio of 2.39 for the entire follow-up
  period

WT
Variant
Higashi et al. JAMA 2002 287
29
Challenges Facing Warfarin Pharmacogenomics

• Despite the strong association between CYP2C9
  genotype and warfarin dose, CYP2C9 genotype
  accounts for only a small portion of the total
  variability in warfarin doses (10-20)
• Need to determine other genetic and non-genetic
  factors that contribute to interindividual
  variability in warfarin doses

30
CYP2D6 Polymorphisms

• CYP2D6 is responsible for the metabolism of a
  number of different drugs
• Antidepressants, antipsychotics, analgesics,
  cardiovascular drugs
• Over 100 polymorphisms in CYP2D6 have been
  identified
• Based on these polymorphisms, patients are
  phenotypically classified as
• Ultrarapid metabolizers (UMs)
• Extensive metabolizers (EMs)
• Poor metabolizers (PMs)

31
CYP2D6 Phenotypes
NEJM 2003 348529
Roden DM et al. Ann Intern Med 2006 145749-57
32
CYP2D6 Polymorphisms and Psychiatric Drug Response

• Increased rate of adverse effects in poor
  metabolizers due to increased plasma
  concentrations of drug
• Fluoxetine (Prozac?) death in child attributed to
  CYP2D6 poor metabolizer genotype
• Side effects of antipsychotic drugs occur more
  frequently in CYP2D6 poor metabolizers
• CYP2D6 poor metabolizers with severe mental
  illness had more adverse drug reactions,
  increased cost of care, and longer hospital stays

33
CYP2D6 and Codeine

• Codeine requires activation by CYP2D6 in order to
  exert its analgesic effect
• Due to genetic polymorphisms, 2-10 of the
  population cannot metabolize codeine and are
  resistant to the analgesic effects
• Interindividual variability exists in the
  adequacy of pain relief when uniform doses of
  codeine are given

34
Strattera (Atomoxetine)

• Treatment of attention deficit hyperactivity
  disorder
• CYP2D6 poor metabolizers have 10-fold higher
  plasma concentrations to a given dose of
  STRATTERA compared with extensive metabolizers
• Approximately 7 of Caucasians are poor
  metabolizers
• Higher blood levels in poor metabolizers may lead
  to a higher rate of some adverse effects of
  STRATTERA

35
CYP2C19 and Proton Pump Inhibitors

• Proton pump inhibitors are used to treat acid
  reflux and stomach ulcers
• Ulcer cure rates using omeprazole and amoxicillin
  by CYP2C19 phenotype
• Cure Rate
• Rapid metabolizers 28.6
• Intermediate metabolizers 60
• Poor metabolizers 100

• Furuta, T. et. al. Ann Intern Med
  19981291027-1030

36
Roche AmpliChip FDA-Approved
37
Roche AmpliChip P450 Test

• The Roche AmpliChip CYP450 Test is intended to
  identify a patient's CYP2D6 and CYP2C19 genotype
  from genomic DNA extracted from a whole blood
  sample.
• Information about CYP2D6 and CYP2C19 genotype
  may be used as an aid to clinicians in
  determining therapeutic strategy and treatment
  dose for therapeutics that are metabolized by the
  CYP2D6 or CYP2C19 gene product.

38
Thiopurine-S-Methyltransferase (TPMT)

• Thiopurine drugs are used to treat cancer
• Acute lymphoblastic leukemia
• TPMT is important for metabolizing thiopurines
• azathioprine, mercaptopurine (6-MP)
• Polymorphisms in the TPMT gene result in
  decreased TPMT enzyme activity
• Decreased TPMT activity predisposes individuals
  to severe, life-threatening toxicities from these
  drugs

39
Variability in TPMT Activity
40
Genotype-Guided 6-MP Dosing
Pharmacogenomics 20023(1)89-98.
41
6-Mercaptopurine Prescribing Information

• There are individuals with an inherited
  deficiency
• of the enzyme thiopurine methyltransferase
• (TPMT) who may be unusually sensitive to the
• myelosuppressive effects of mercaptopurine and
• prone to developing rapid bone marrow
• suppression following the initiation of
  treatment.
• Substantial dosage reductions may be required to
• avoid the development of life-threatening bone
• marrow suppression in these patients.

42
Imuran Prescribing Information

• TPMT genotyping or phenotyping can be used to
  identify patients with absent or reduced TPMT
  activity.
• Patients with low or absent TPMT activity are at
  an increased risk of developing severe,
  life-threatening myelotoxicity from IMURAN if
  conventional doses are given.
• Physicians may consider alternative therapies
  for patients who have low or absent TPMT activity
  (homozygous for non-functional alleles). IMURAN
  should be administered with caution to patients
  having one non-functional allele (heterozygous)
  who are at risk for reduced TPMT activity that
  may lead to toxicity if conventional doses are
  given. Dosage reduction is recommended in
  patients with reduced TPMT activity.

43
TPMT and Thioguanines

• Clinical implications
• Genetic testing for TPMT is routine practice at
  some cancer centers for protocols involving
  thiopurine drugs
• CLIA approved test available
• Implications for cancer, transplant, rheumatoid
  arthritis, lupus, dermatology, and Crohns
  disease treatment

44
Drug Target Pharmacogenomics
45
Drug Target Pharmacogenomics

• Direct protein target of drug
• Receptor
• Enzyme
• Proteins involved in pharmacologic response
• Signal transduction proteins or downstream
  proteins
• Polymorphisms associated with
• disease risk
• Disease-modifying polymorphisms
• Treatment-modifying polymorphisms
• POLYGENIC

46
Complexity of Drug Effect
47
Assessing Phenotype in Drug Target
Pharmacogenomics

• DepressionSymptom rating scales
• Indirect measure of drug response
• Inter-rater reliability
• HypertensionBlood pressure
• Minute to minute and diurnal variability
• Influence of environmental factors (e.g. lack of
  rest before measurement)
• DiabetesBlood glucose
• Diurnal variation in blood glucose
• Influence of environmental factors (e.g.
  diet/exercise)

48
Comparison

• Drug Metabolism Pgx
• Polymorphisms often lead to non-functional or
  absent proteins
• Distinct phenotypes
• Bimodal/trimodal distribution
• Phenotypes are easily measured
• Drug concentration
• In vitro catalytic activity

• Drug Target Pgx
• Polymorphisms usually dont result in lack of
  protein function
• Subtle effects
• Differences in phenotypes are smaller
• Measurement of phenotypes is difficult
• Imprecise and variable
• Failure to consider haplotypes

Johnson JA and Lima JJ. Pharmacogenetics 2003
13525-534
49
Examples of Drug Target Pharmacogenomics
Evans WE. NEJM 2003 348538-48
50
Examples of Disease or Treatment Modifying
Pharmacogenomics
Evans WE. NEJM 2003 348538-48
51
Beta-blockers and Hypertension (HTN)

• HTN is the most prevalent chronic disease in the
  US and a contributor to morbidity and mortality
• Beta-blockers are first-line agent in the
  treatment of HTN
• Marked variability in response to beta-blockers
• 30-60 of patients fail to achieve adequate blood
  pressure lowering with beta-blockers
• Common beta-blockers used in HTN
• Metoprolol
• Atenolol

52
Beta-1 Adrenergic Receptor
Codon 49 Ser?Gly
Codon 389 Arg?Gly
Podlowski, et al. J Mol Med 20007890.
53
Beta-1 Receptor Polymorphisms and Response to
Metoprolol
Johnson JA et al. Clin Pharmacol Ther 2003
7444-52
54
Beta-2 Adrenergic Receptor Polymorphisms and
Response to Albuterol in Asthma

• Hyperreactivity of the airways is the hallmark of
  asthma
• Airway smooth muscle contains beta-2 receptors
  that produce broncodilation
• Albuterol is a beta-2 agonist that is used in the
  treatment of asthma
• Produces smooth muscle cell relaxation and
  bronchodilation
• Forced expiratory volume in 1 second (FEV1)
• Phenotypic measure of response

55
Beta-2 Polymorphisms and Response to Albuterol

• 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

Lima JJ. Clin Pharmacol Ther 1999 65519-25
56
VKOR and Warfarin

• Warfarin works by inhibiting Vitamin K Epoxide
  Reductase (VKOR)
• VKOR helps recycle vitamin K which is important
  in proper functioning of clotting factors
• By inhibiting VKOR, warfarin alters the vitamin K
  cycle and results in the production of inactive
  clotting factors
• Polymorphisms exist in the gene for VKOR (VKORC1)

57
VKORC1 Genotype and Warfarin Dose Requirements
46 mg/wk
33 mg/wk
21 mg/wk
G/G G/A A/A
58
Warfarin Pharmacogenomics

• CYP2C9 SNPs account for a small amount of
  variability in warfarin doses (10)
• VKORC1 SNPs explain a larger portion of
  variability in warfarin doses (20-25)
• Almost 50 of variability in warfarin doses can
  be explained by a combination of factors
• VKORC1 SNPs
• CYP2C9 SNPs
• Non-genetic factors (age, weight, concomitant
  drugs, concomitant disease states)

59
Warfarin Pharmacogenomics

• Current Status
• Develop and validate dosing algorithms to that
  include VKORC1 genetic information, CYP2C9
  genetic information, and non-genetic factors
  (e.g., age, weight, concomitant drugs,
  concomitant disease states)
• Test if dosing warfarin based on genotype is
  better than the usual care approach

60
Abacavir Hypersensitivity

• Antiretroviral used for treatment of HIV
• 5 of patients experience hypersensitivity
  reactions to the drug
• Hypersensitivity is fatal in rare cases
• Hypersensitivity reaction starts with severe GI
  symptoms, followed by fever and rash
• Discontinuation of drug reverses symptoms
• Re-challenge of abacavir in hypersensitive
  individuals can result in life-threatening low
  blood pressure or death

Lancet 2002359727-32.
61
Abacavir Hypersensitivity

• Hypersensitivity typically believed to be an
  immunologic reaction
• Hypersensitivity might be genetically linked, and
  thus predictable
• Major histocompatibility proteins (MHC)
  investigated because of known links in other
  immune responses and allergic reactions

62
Genetics of Abacavir Hypersensitivity
Western HIV Australia HIV Cohort Study

• Patients with the HLA-B5701 variant were 117
  times more likely to be hypersensitive to
  abacavir than those who did not have the variant
• 13 patients had 3 linked genetic variants
  (5701, DR7, DQ3) and all patients were abacavir
  hypersensitive
• All abacavir hypersensitive patients were
  Caucasian, therefore
• studies in other racial groups are needed

63
Disease Risk Polymorphisms

• Polymorphisms can predispose individuals to a
  disease or increase the risk for disease
• If a drug with a known adverse effect is given to
  a person with a genetic susceptibility to that
  adverse effect, there is an increased likelihood
  for that adverse effect

64
Clotting Factor Polymorphisms, Blood Clots, and
Oral Contraceptive Pills

• Polymorphisms exist in clotting factor genes
• Oral contraceptive pills alone are associated
  with an increased risk of blood clots
• Women who have clotting factor polymorphisms are
  at an even greater risk for blood clots if they
  receive oral contraceptive pills

65
Oral Contraceptive Pills and Blood Clots
Heterozygotes
Patients on OCP who are homozygous for Factor V
Leiden have 50 to100-fold increased risk of VTE
Martinelli I. Pharmacogenetics 2003 13589-594
66
A Different Aspect of Drug Target
Pharmacogenomics

• In all of the examples thus far, the drug target
  has been a human protein
• The gene encoding that human protein has
  generally NOT undergone mutation during the
  patients life
• However, in the areas of infectious diseases and
  cancer, the drug target is often a non-human
  protein
• Cancer Tumor DNA
• Infectious Diseases Viral genotype
• e.g., HIV, HBV, HCV

67
HER-2 Protein and Herceptin

• Herceptin (trastuzumab)
• Metastatic breast cancer
• Targets tumor cells that over-express the human
  epidermal growth factor receptor 2 (HER2) protein
• Best response attained in women who over-express
  the HER2 protein
• HER-2 over-expression in breast cancer cells
  should be done before patients receive the drug

68
Herceptin Prescribing Information

• HERCEPTIN (Trastuzumab) as a single agent is
  indicated for the treatment of patients with
  metastatic breast cancer whose tumors overexpress
  the HER2 protein and who have received one or
  more chemotherapy regimens for their metastatic
  disease.
• HERCEPTIN should be used in patients whose tumors
  have been evaluated with an assay validated to
  predict HER2 protein overexpression

69
Hepatitis C

• Interferon-?-2b and ribavirin are used to treat
  patients with hepatitis C virus
• Different mutations exist in the hepatitis C
  virus
• Knowledge of a persons hepatitis C genotype may
  help play a role in the therapeutic
  decision-making process

70
HIV and Antiretroviral Drugs

• Resistance to antiretroviral agents hinders the
  management of HIV disease
• In the virus, mutations occur which confer drug
  resistance
• Knowledge of viral genotype (or phenotype) can
  help guide the selection of antiretroviral
  therapy

71
Challenges Facing the Field of Pharmacogenomics

• Multiple studies, but literature is inconclusive
  in some instances
• Genetics accounts for an insufficient percentage
  of response variability for a given drug
• Few studies documenting genotype-guided therapy
  is better than the usual care approach
• Few point-of-care tests available to determine
  a persons genetic make-up or protein expression

72
Potential Reasons for Discrepancies

• Inadequately powered studies
• Studying different drug response phenotypes
• Studying different patient populations
  (differences in allele frequencies)
• Problems precisely measuring phenotype
• Subtlety of functional effects of polymorphisms
• Focus on single SNPs instead of haplotypes
• Failure to consider the complexity of drug
  response

Johnson JA and Lima JJ. Pharmacogenetics 2003
13525-534
73
(No Transcript)
74
(No Transcript)
75
Pharmacogenetics and Pharmacogenomics Knowledge
Base (PharmGKB)

• Publicly accessible knowledge base
• www.pharmgkb.org
• Goal establish the definitive source of
  information about the interaction of genetic
  variability and drug response
• Store and organize primary genotyping data
• Correlate phenotypic measures of drug response
  with genotypic data
• Curate major findings of the published literature
• Provide information about complex drug pathways
• Highlight genes that are critical for
  understanding pharmacogenomics

76
Role of Pharmacogenomics in the Drug
Development Process

• 80 of products that enter the development
  pipeline FAIL to make it to market
• Pharmacogenomics may contribute to a smarter
  drug development process
• Allow for the prediction of efficacy/toxicity
  during clinical development
• Make the process more efficient by decreasing the
  number of patients required to show efficacy in
  clinical trials
• Decrease costs and time to bring drug to market

77
Pharmacogenomic Paradigm in the Drug Development
Process
Current Options Options with Pharmacogenomics
High
Proportion of patients showing poor or no response
Low
78
Personalized Medicine and the Pharmaceutical
Industry

• Targeted Therapies
• Herceptin treatment of HER2 positive metastatic
  breast cancer
• Gleevec treatment for patients with
  Philadelphia chromosome-positive chronic myeloid
  leukemia
• Erlotinib treatment for non-small cell lung
  cancer
• Most effective in epidermal growth factor
  receptor positive tumors
• Maraviroc (not approved) treatment for HIV
• Studies have incorporated a screening process for
  different receptors that HIV uses to gain access
  to cells
• Iloperidone (not approved) schizophrenia
  treatment
• Company identified a genetic marker that predicts
  a good response to the drug

79
Pharmacogenomic Paradigm in the Pharmaceutical
Industry
Efficacy prediction
Common side effect prediction
Rare side effect prediction
Market expansion
80
FDA and Pharmacogenomics

• Traditionally, industry has been hesitant to
  submit pharmacogenomic data due to fears of
• Delays in drug development
• Request for additional clinical studies
• Potentially put clinical trials on hold
• FDA published Draft Guidance for Industry
  Pharmacogenomic Data Submission in 2003.
  (currently under revision)
• Set criteria for Voluntary Genomic Data
  Submission (VGDS)

http//www.fda.gov/cder/guidance/5900dft.pdf
81
Pharmacogenomics Information in the Published
Literature
Zineh I et al. Ann Pharmacother. 2006 40
639-44
82
Pharmacogenomics Information in FDA-Approved
Prescribing Information
Zineh I et al. Pharmacogenomics J 2004 1-5
83
Moving Pharmacogenomics to Clinical Practice
Document Pgx superiority Pgx-guided versus
usual care
Documenting sufficient variability to predict
clinical utility
Studies that mimic clinical practice
Proof-of-concept clinical studies
In vitro functional studies
Identify sequence variability in candidate genes
Johnson JA. Trends in Genetics 2003 19 660-66
84
The Future of Pharmacogenomics

• Genome wide approach versus candidate gene
  approach
• Thousands of SNPs
• Thousands of patients
• Replication studies
• Sophisticated databases housing pharmacogenomic
  information
• Drug selection and dosing algorithms
  incorporating non-genetic and genetic information
• Point of care genetic testing

85
"Here's my sequence..."
The New Yorker
86
Personalized medicine elusive dream or
imminent reality?In summary it is both.

• Larry Lesko, Director of the FDA Office of
  Clinical Pharmacology and Biopharmaceutics

• Clin Pharmacol Ther 2007 807-816