Pharmacogenetics and Pharmacogenomics

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Pharmacogenetics and Pharmacogenomics

• Kevin Zbuk, MD
• Medical Oncologist
• Juravinski Cancer Centre
• McMaster University

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Outline

• Introduction and definitions
• Basic concepts
• Case studies
• Conclusions

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Pharmacogenetic versus Pharmacogenomic

• No universally accepted definitions of either
• Often used interchangeably
• Pharmacogenetics used for more than 40 years to
  denote the science about how heritability affects
  the response to drugs.
• Pharmacogenomics is new science about how the
  systematic identification of all the human genes,
  their products, interindividual variation,
  intraindividual variation in expression and
  function over time affects drug
  response/metabolism etc.
• The term pharmacogenomics was coined in
  connection with the human genome project
• Most use pharmacogenetics to depict the study of
  single genes and their effects on interindividual
  differences in (mainly) drug metabolising
  enzymes, and pharmacogenomics to depict the study
  of not just single genes but the functions and
  interactions of all genes in the genome in the
  overall variability of drugs response

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Pharmacogenetics

• Pharmacogenetics is the study of how genetic
  variations affect the disposition of drugs,
  including their metabolism and transport and
  their safety and efficacy
• J. Hoskins et. al NRC 2009

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Pharmacogenetics involves both PK and PD

• Pharmacokinetic
• The process by which a drug is absorbed,
  distributed, metabolized, and eliminated by the
  body
• Pharmacodynamic
• the biochemical and physiological effects of
  drugs and the mechanisms of their actions

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Goals of Pharmacogen(etics)omics

• Maximize drug efficacy
• Minimize drug toxicity
• Predict patients who will respond to intervention
• Aid in new drug development

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The Hope of Pharmacogenomics

• Individuals genetic makeup with allow selective
  use of medications such that
• Efficacy maximized
• Side effect minimized

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This is the hope/hype
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In the Beginning

• Mendelian genetics single gene single disease
• single wild type allele and single disease allele
• Patterns of inheritance included autosomal
  dominant (need only one disease allele) and
  autosomal recessive (need two disease alleles)
• Followed soon thereafter by additive
  (co-dominant) model
• Both alleles contribute to phenotype

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Dominant/Recessive
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Co-dominance
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Empiric observations suggesting Pharmacogenetics
important

• Clinical response to many drugs varies widely
  amongst individuals
• Same drug-gt same dose -gt same indication in
  different individuals
• Some respond
• Some dont
• Some dont respond and have serious toxicity

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EARLY PK EXAMPLES
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The beginning of pharmacogenetics

• 1950s
• Inheritance might explain variation in
  individuals response and adverse effects from
  drugs Motulsty
• Pharmacogenetics defined as study of role of
  Genetics in drug response Vogel
• Most of studies for next several decades of high
  penetrance monogenic gene-drug interactions
• Def Monogenetic disease. Mutation at single
  locus sufficient to result in disorder

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Penetrance

• Penetrance of a disease-causing mutation is the
  proportion of individuals with the mutation who
  exhibit clinical symptoms.
• Eg. if a mutation in the gene responsible for a
  particular autosomal dominantdisorder has 95
  penetrance, then 95 of those with the mutation
  will develop the disease, while 5 will not.

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Victor McKusick

• Established Online Mendelian Inheritance in Man
  in early 80s
• Categorized majority of Mendelian Disorders
• Became very clear that there are many different
  disease alleles for many disorders (allelic
  heterogeneity)
• Recently many disorders have associated modifier
  genes that modify disease phenotype
• Eg. Age-of-onset and severity

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Example 1- Success of Pharmacogenetics in Oncology

• TPMT

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TPMT

• Main metabolizer of chemotherapeutic agents 6MP
  and azothiopurine (used mainly in blood based
  malignancies)
• TPMT deficiency leads to severe toxicity
  associated with treatment (potential mortality)

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TPMT enzyme activity distribution
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Hematologic toxicity according to TPMT genotype
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Evans Nature Reviews Cancer 2006
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FDA approved pharmacogenetic tests
Gene Drug Consequence
TPMT 6MP Toxicity
CYP2D6 Tamoxifen Decreased efficacy
UGT1A1 Irinotecan Toxicity
CYP2D6 Codeine Ineffective analgesia
These genes all modulate Pharmokinetics
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Contribution of High Penetrance Monogenic Model
to PG

• Contribution likely not as large as initially
  anticipated
• For most pharmacologic traits might be 15-20 at
  most
• Could consider this penetrance
• Redundancy likely a major contributing factor
• MANY ENZYMES INVOLVED IN DRUG METABOLISM WITH
  MANY ALTERNATE PATHWAYS
• Dichotomous disease versus quantitative trait
• Much more likely polygenic model with
  gene-environment interactions

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Some of it aint genetic

• Age
• Co-morbidities
• Renal and hepatic function (dysfunction)
• Concomitant medications
• Diet and smoking

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Common Disease Common Variant Hypothesis

• Most complex diseases are strongly influenced by
  combination of frequent alleles that each only
  exert modest effect

Polygenic Model (lnheritance)
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Approach to polygenic pharmacogenomic traits
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Polygenic Model and PG

• Elucidation unlikely possible before advances in
  genomics
• Technologic advances
• High throughput sequencing of DNA
• Affordable genotyping of 100ks to 1-2M SNPs
• Genomic knowledge advances
• Especially Human Genome Project and HapMap
  Projects

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Cost of Genotyping

• In 2005 (5 years ago!)
• 1600 to genotype 250K SNPs in one individual
• 2009
• 250 to genotype gt1Million SNPs
• 2014
• -200-250 to genotype gt5 millions SNPs

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Hapmap project

• There are an estimated 10 million SNPs with MAF
  gt1
• Hapmap project genotyped Chinese, Japanese,
  African and European individuals (families)

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HapMap Project
Phase 1 Phase 2 Phase 3
Samples POP panels 269 samples (4 panels) 270 samples (4 panels) 1,115 samples (11 panels)
Genotyping centers HapMap International Consortium Perlegen Broad Sanger
Unique QC SNPs 1.1 M 3.8 M (phase III) 1.6 M (Affy 6.0 Illumina 1M)
Reference Nature (2005) 437p1299 Nature (2007) 449p851 Draft Rel. 3 (2010)
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A more in depth look at PK in clinical practice

• Tamoxifen use and CYP2D6

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Tamoxifen metabolism

• Needs to be converted to endoxifen to be active
• catalysed by the polymorphic enzyme cytochrome
  P450 2D6 (CYP2D6)
• 6-10 European population deficient in this
  enzyme
• Efficacy of tamoxifen likely low in this
  population
• Suggests consider alterative treatments

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J. Hoskins et. al NRC 2009
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About the CYPs

• Membrane bound enzymatic proteins
• Involved in oxidation, peroxidation and reductive
  metabolism
• Responsible for gt90 of drug transformation
• Greater than 50 different CYP genes encoding 50
  different proteins
• CYP2D6 present mainly in liver and a major player
  in drug metabolism from antidepressants to
  antihypertensive to chemotherapy

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Evolution of CYP nomenclature

• Initially astute clinical observation of unusual
  drug response
• Such responses then found to be heritable
• Early example of phenotype to genotype approach
• CYP2D6 polymorphism the first described
• Increasing recognition of poor metabolizer
  phenotype occurred at time that genotyping
  technology in evolution

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About CYP2D6
P arm
Location 22q 13.1
Q arm
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CYP2D6 alleles

• There are gt70 described in this gene
• Bottom line variants either cause no change,
  decrease somewhat, or significantly decrease
  metabolism
• Extensive metabolizers ( EM), intermediate (IM)
  metabolizers, and poor metabolizers (PM)
• EM is the standard metabolism allele against
  which others are compared (consider it the wild
  type)

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Hoskins et al. Nature Reviews Cancer 2009
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CYP2D6 alleles Copy Number Variation

• Throughout the genome there are areas of DNA that
  are represented in variable copies in individuals
  (CNV)
• CYP2D6 is one such area
• Up to 16 copies seen in some individuals
• NORMAL VARIANT
• ULTRARAPID METABOLIZERS

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Consequence of CYP2D6 alleles?

• EM/EM or EM/IM(PM) normal metabolizers
• IM/IM or IM/PM intermediate metabolizers
• PM/PM poor metabolizers
• Poor/(Intermediate) metabolizers have much lower
  levels of endoxifen than intermediate/ rapid
  metabolizers

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CYP2D6 Genotype and clinical outcomes

• Several (small trials) have suggested decreased
  efficacy of Tamoxifen in poor (intermediate)
  metabolizers both in adjuvant therapy and in
  treatment of metastatic disease (see Hoskins NRC
  2009 for details)
• All retrospective
• Largest was only statistically significant
  association in univariate analysis
• In additions several trials have not confirmed
  these results

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Reasons for discordant results in CYP2D6 trials

• Did not genotype many of the rarer poor
  metabolizer alleles
• Did not account for concurrent use of other drugs
  metabolized by CYP2D6 in many cases
• Different dose of Tamoxifen in several trials
• Did not assay endoxifen levels
• Power (poor metabolizers rare)
• Unknown variants in other genes whose products
  involved in tamoxifen metabolism

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So what is needed to clarify the issue of
relevance of CYP2D6 genotype and clinical
relevance?

• Large randomized trial that compares standard
  dosing of tamoxifen to genotype adjusted dosing
• Until that point clinical utility of testing
  (commerically available) unclear
• Should recommend avoiding SSRIs that inhibit
  CYP2D6 significantly (see later)

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Provocative thoughts

• In post-menopausal breast cancer tamoxifen is
  falling out of favor due to the efficacy of
  Aromatase Inhibitors (inhibit extragonadal
  production of estrogen)
• AI shows increased efficacy c/w tamoxifen
• BUT MUCH MORE EXPENSIVE AND DIFFERENT S/E PROFILE
  
• Some suggestion that increased efficacy of AI
  completely explained by decreased efficacy of
  Tamoxifen in CYP2D6 IM and PM
• Punglia (2008) JNCI

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More relevant to pre-menopausal woman

• Cant use AI alone
• In poor metabolizer could consider
• Increased dose???
• Alternative estrogen receptor modulator not
  metabolized by CYP2D6 (eg. raloxifen)
• Consider AI with ovarian ablation (chemical or
  otherwise)

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Ethnic Differences in IM and PM of CYP2D6

• PM alleles more common in European population
• IM alleles much more common in East Asian and
  African population
• In East Asians Intermediate Metabolizers show
  similar in vitro CYP2D6 activity c/w Poor
  Metabolizers in European populations
• Gene-gene or gene-environment interactions

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Drug Co-administration

• Antidepressant use common in breast cancer
  patients
• Depression more common in breast cancer patients
  and antidepressant often used to treat how
  flashes associated with tamoxifen use
• SSRIs (eg. Fluoxetine and paroxetine) inhibit
  CYP2D6
• Level of inhibition varies between different
  drugs with paroxetine having most inhibition and
  venlafaxine causing none
• Kelly et al. BMJ 2010
• Population based cohort study of women receiving
  tamoxifen adjuvantly for treatment breast cancer
• Mortality from breast cancer increased in group
  using paroxtetine concurrent with tamoxifen

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Irinotecan PK example in Colon Cancer

• Excreted after conjugation (glucuronidation) by
  UGT1A1
• TATA element (consists of TA repeats) in UGT1A1
  promoter shows correlation with transcription
  levels
• More repeats lower transcription levels
• An example of a non-SNP variant with clinical
  relevance
• Homozygosity for 7-repeat allele, also known as
  UGT1A128 associated with severe toxicity
  (diarrhea and low WBC counts mainly)
• Results have been somewhat inconsistent but
  meta-analysis confirms same especially with
  higher doses of Irinotecan
• Homozygosity only in 5-15 of individuals

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PD example in Colon Cancer Treatment

• EGFR inhibitors used in treatment of advanced
  colon cancer (eg. Cetuximab)
• Tumors with k-RAS (and probably BRAF) mutations
  will NOT respond to EGFR inhibition

Nature Rev. Cancer July 2009
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Review Paper by Pare et al.
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Effect of Clopidogrel as Compared with Placebo on
Clinical Outcomes among Patients with Acute
Coronary Syndromes in the CURE trial, Stratified
According to Metabolizer Phenotype.
Paré G et al. N Engl J Med 20103631704-1714
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KaplanMeier Curves for Event-free Survival
According to CYP2C19 Loss-of-Function and
Gain-of-Function Allele Carrier Status among
European and Latin American Patients with Acute
Coronary Syndromes in the CURE Trial.
Paré G et al. N Engl J Med 20103631704-1714
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Effect of Clopidogrel as Compared with Placebo on
Clinical Outcomes among Patients with Atrial
Fibrillation in ACTIVE A, Stratified According to
Metabolizer Phenotype.
Paré G et al. N Engl J Med 20103631704-1714
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KaplanMeier Curves for Event-free Survival
According to CYP2C19 Loss-of-Function and
Gain-of-Function Allele Carrier Status among
European Patients with Atrial Fibrillation in
ACTIVE A.
Paré G et al. N Engl J Med 20103631704-1714
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Baseline Characteristics of Genotyped Patients in
the CURE and ACTIVE A Trials.
Paré G et al. N Engl J Med 20103631704-1714
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Why is pharmacogenomics not widely utilized in
the clinic

• It required a shift in clinician attitude and
  beliefs not one dose fits all
• Paucity of studies demonstrating improved
  clinical benefit from use of pharmacogenomic data
• Still much to be learned
• Even some of the black block warnings currently
  on drug labels may be overcalls of importance
• Genome wide interrogation will likely be
  important to get the entire picture

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Conclusion

• Genetic variation contributes to inter-individual
  differences in drug response phenotype at every
  pharmacologic step
• Through individualized treatments,
  pharmacogenetics and pharmacogenomics are
  expected to lead to
• Better, safer drugs the first time
• More accurate methods of determining appropriate
  drug dosages
• Pharmacogenomics offers unprecedented
  opportunities to understand the genetic
  architecture of drug response
• HOWEVER IN MANY CASES NOT YET READY FOR PRIME
  TIME!!!