introduction to pharmacogenomics
TRANSCRIPT
8/11/2019 Introduction to Pharmacogenomics
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Genes and Drugs
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OUTLINE
– How do we know if a patient will respond to a drug?
– What are the response rates for different classes of drugs?
– How are doses determined?
– Why does drug response vary?
– Genetic variation• What is it?• How do you measure it?• How extensive is it?• Pharmacogenomics: genetic variation and drug response
– Examples• Gefitinib• Warfarin
– Pharmacogenomics – costs and benefits
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OUTLINE
– How do we know if a patient will respond to a drug?
– What are the response rates for different classes of drugs?
– How are doses determined?
– Why does drug response vary?
– Genetic variation• What is it?• How do you measure it?• How extensive is it?• Pharmacogenomics: genetic variation and drug response
– Examples• Gefitinib• Warfarin
– Pharmacogenomics – costs and benefits
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Some examples of drug response rates
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OUTLINE
– How do we know if a patient will respond to a drug?
– What are the response rates for different classes of drugs?
– How are doses determined?
– Why does drug response vary?
– Genetic variation• What is it?• How do you measure it?• How extensive is it?• Pharmacogenomics: genetic variation and drug response
– Examples• Gefitinib• Warfarin
– Pharmacogenomics – costs and benefits
8/11/2019 Introduction to Pharmacogenomics
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Dose determination
– Phase I clinical trials (safety)• 20 to 80 healthy volunteers• Determine max tolerable dose
– Phase II clinical trials (efficacy)• Several hundred patients• estimate therapeutic dose range
– Drugs approved with a specific indication and dose range
– Phase III monitoring.
– Dose that patients actually receive depends on… • Prior treatment history of patient (drug naïve?)• Physicians experience with prescribing drug• Empirical knowledge of appropriate dose• In practice – start low, ramp to ~80% of recommended dose before trying
different drug• Liability issues
– No clinical trials are done to study dose escalation
– Therapeutic drug monitoring
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OUTLINE
– How do we know if a patient will respond to a drug?
– What are the response rates for different classes of drugs?
– How are doses determined?
– Why does drug response vary?
– Genetic variation• What is it?• How do you measure it?• How extensive is it?• Pharmacogenomics: genetic variation and drug response
– Examples• Gefitinib• Warfarin
– Pharmacogenomics – costs and benefits
8/11/2019 Introduction to Pharmacogenomics
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Potential causes of variability in drug effects:
• Pathogenesis and the severity of the disease beingtreated.
• Drug interactions from concomitant treatments(plasma protein binding, metabolism)
• Individual’s age, gender, lifestyle (includingenvironmental factors), behavior, nutritional state,
renal and liver function, and concomitant illnesses.
• Genetic variation
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A patient’s response to a drug may depend onfactors that can vary according to the allelesthat an individual carries, including
Pharmacokinetic factors
• Absorption
• Distribution
• Metabolism• Elimination
Pharmacodynamic factors
• target proteins
• downstream messengers
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Phase II metabolism (conjugation)
Substrate is phase I reaction product, or other endogenouscompound ( eg. steroid hormones)
Congugaton of highly polar glucuronide enhances watersolubility/decreases lipid solubility and thereby promotesexcretion
Fewer genes and functional variants than P450s
Gtxase
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EM
PM
EM = extensivemetabolizers
PM = poormetabolizers
Distributionof metabolic
efficiency
Metabolic ratio
= [parent]/[metabolite]
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OUTLINE
– How do we know if a patient will respond to a drug?
– What are the response rates for different classes of drugs?
– How are doses determined?
– Why does drug response vary?
– Genetic variation• What is it?• How do you measure it?• How extensive is it?• Pharmacogenomics: genetic variation and drug response
– Examples• Gefitinib• Warfarin
– Pharmacogenomics – costs and benefits
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Variation in the genome most relevant
to pharmacogenomics:
• Insertions/deletions (small and large)
• Single nucleotide polymorphisms
(SNPs)
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Copy NumberPolymorphisms inHuman Genome
gains
losses
• 39 healthy
unrelated individuals
• 255 loci
• 24 variants present
in >10% of
individuals
Iafrate et al., Nat Genet.36, 949 (2004)
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SNPs are the most commonly occurringgenetic differences
ACGCCTTGACGAAGCTTAC
ACGCCTTGACGAT GCTTAC
SNPs are single base pair positions in genomic DNAat which different sequence alternatives (alleles)
exist wherein the least frequent allele has anabundance of 1% or greater
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SNPs are estimated to occur throughout thegenome at a rate of between 3 and 6 per
1000 base pairs
– Any individual selected at random contains~25% of human variation
– ~90% of snps in any given individual are presentin pop’n at large
– There are expected to be a total of 10-20MSNPs in human population
Bi h i t f SNP G t i
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Biochemistry of SNP Genotyping
MassARRAY™ Affymetix SNP Chip
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MassARRAY™
Compact System
Affymetix SNP Chip
ABI 7900
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Pharmacogenomics
The effects of an individual’s genotype on thepharmacokinetics and pharmacodynamics ofdrug action.
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OUTLINE
– How do we know if a patient will respond to a drug?
– What are the response rates for different classes of drugs?
– How are doses determined?
– Why does drug response vary?
– Genetic variation• What is it?• How do you measure it?• How extensive is it?• Pharmacogenomics: genetic variation and drug response
– Examples• Gefitinib• Warfarin
– Pharmacogenomics – costs and benefits
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Gefitinib (Iressa)
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Gefitinib
•
Epidermal Growth Factor Receptor over-expressed in 40-80% of Non-Small-CellLung Carcinomas
•EGFR signaling triggered by binding of growth factors, resulting in dimerization of
receptor, auto/trans phosphorylation via tyrosine kinase domain, recruitment of
downstream effectors and activation of cell prolioferation/survival programs
•Gefitinib inhibits EGFR by blocking ATP cleft, thereby preventing activation by
autophosphorylation
•Tumor responses seen in only ~10% of patients with chemotherapy resistant
advanced NSCLC
• A subgroup of patients with NSCLC have specific mutations in the EGFR gene
that constitutively activate the receptor, and confer sensitivity ot Gefitinib
Lynch TJ et al., NEJM 350,2129; Paez JG et al., Science, 304,1497
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Gefitinib•25/275 patients at Mass General identified as being responsive. EGFR sequenced in 9
responsive patients.
f b
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Gefitinib
• All mutations in kinase domain
•Matched tissue showed wild type sequence. No mutations seen in 7 non-
responsive cases analysed
•Heterozygous mutations seen in 2 cases. Dominant gain of function mutation
•Heterologous expression in Cos-7 cells shows mutant receptors (IC50 = 0.015uM)
more sensitive to inhibition by gefitinib than wild type (IC50 = 0.1uM).
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Gefitinib
Conclusions
•Only a subgroup of NSCLC tumors harbour EGFR mutations.
•This subtype of NSCLC sensitive to genfitinib
•Patients should be screened for EGFR mutations, and if they have them,
be given gefitinib as first line therapy.
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Warfarin (Coumadin)
W f i
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Warfarin
• Anticoagulant of choice in North America for cardivascular disease,
thromboembolic disease, and prophylactic post-surgery application
mechanism
• activation of coagulation factors II, VII, IX and X by carboxylation
requires vitamin K
• vitK generated by vitK-epoxide-reductase.
• warfarin (and other oral anticoagulants) inhibits this enzyme
complex.
•15th most prescribed drug and 1st in category of accidents and adverse
reactions (bleeding)
•Very narrow therapeutic index and individualized dosing mandatory.
Effective daily dose 0.5 to 80mg
•Dosing determined by patient history and physical exam, in conjunction
with INR (international normalization ratio. In-vitro clotting time versus
standard reference)
Warfarin
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Warfarin• genetic factors
influencing
warfarin
response
unknown.
• genetic data
may help
determining
correct doseand preventing
adverse
reactions
• present
study: type 14genes in 1000+
patients and
associate
variants with
warfarin
response
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OUTLINE
– How do we know if a patient will respond to a drug?
– What are the response rates for different classes of drugs?
– How are doses determined?
– Why does drug response vary?
– Genetic variation• What is it?• How do you measure it?• How extensive is it?• Pharmacogenomics: genetic variation and drug response
– Examples• Gefitinib• Warfarin
– Pharmacogenomics – costs and benefits
8/11/2019 Introduction to Pharmacogenomics
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• Logistics - how do you obtain genotypes clinically and how do you
manage this information
• cost
• How deterministic is a genotype
• Do primary caregivers know how to interpret and apply these data?
• Fractionating market not immediately desirable for drug makers