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!!!