Post on 16-Dec-2015
Pharmacogenetics and Pharmacogenomics
Kevin Zbuk, MDMedical Oncologist
Juravinski Cancer CentreMcMaster University
Outline
• Introduction and definitions• Basic concepts• Case studies• Conclusions
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
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
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”
Goals of Pharmacogen(etics)omics
• Maximize drug efficacy• Minimize drug toxicity• Predict patients who will respond to
intervention• Aid in new drug development
The Hope of Pharmacogenomics
• Individuals genetic makeup with allow selective use of medications such that– Efficacy maximized– Side effect minimized
This is the hope/hype
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
Dominant/Recessive
Co-dominance
Empiric observations suggesting Pharmacogenetics important
• Clinical response to many drugs varies widely amongst individuals
• Same drug-> same dose -> same indication in different individuals– Some respond– Some don’t– Some don’t respond and have serious toxicity
EARLY PK EXAMPLES
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
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.
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
Example 1- Success of Pharmacogenetics in Oncology
TPMT
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)
TPMT enzyme activity distribution
Hematologic toxicity according to TPMT genotype
Evans Nature Reviews Cancer 2006
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
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
Some of it ain’t genetic
• Age• Co-morbidities• Renal and hepatic function (dysfunction)• Concomitant medications• Diet and smoking
Common Disease Common Variant Hypothesis
• Most complex diseases are strongly influenced by combination of frequent alleles that each only exert modest effect
Approach to polygenic pharmacogenomic traits
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
Cost of Genotyping
• In 2005 (5 years ago!)– $1600 to genotype 250K SNPs in one individual
• 2009– $250 to genotype >1Million SNPs
• 2014 -$200-250 to genotype >5 millions SNPs
Hapmap project
• There are an estimated 10 million SNPs with MAF >1%
• Hapmap project genotyped Chinese, Japanese, African and European individuals (families)
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 I+II)
1.6 M (Affy 6.0 & Illumina 1M)
Reference Nature (2005) 437:p1299
Nature (2007) 449:p851
Draft Rel. 3 (2010)
A more in depth look at PK in clinical practice
Tamoxifen use and CYP2D6
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
J. Hoskins et. al NRC 2009
About the CYPs
• Membrane bound enzymatic proteins– Involved in oxidation, peroxidation and reductive
metabolism – Responsible for >90% 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
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
About CYP2D6
Location 22q 13.1
P arm
Q arm
CYP2D6 alleles
• There are >70 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)
Hoskins et al. Nature Reviews Cancer 2009
CYP2D6 allelesCopy 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
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
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
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
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)
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
More relevant to pre-menopausal woman
• Can’t 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)
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
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
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 UGT1A1*28 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
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
Review Paper by Pare et al.
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 2010;363:1704-1714
Kaplan–Meier 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 2010;363:1704-1714
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 2010;363:1704-1714
Kaplan–Meier 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 2010;363:1704-1714
Baseline Characteristics of Genotyped Patients in the CURE and ACTIVE A Trials.
Paré G et al. N Engl J Med 2010;363:1704-1714
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
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!!!