Introduction to Pharmacogenomics

8/11/2019 Introduction to Pharmacogenomics

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Genes and Drugs



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– 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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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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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



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







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



EM

PM

EM = extensivemetabolizers

PM = poormetabolizers

Distributionof metabolic

efficiency

Metabolic ratio

= [parent]/[metabolite]



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Variation in the genome most relevant

to pharmacogenomics:

• Insertions/deletions (small and large)

• Single nucleotide polymorphisms

(SNPs)



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)





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



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



Biochemistry of SNP Genotyping

MassARRAY™ Affymetix SNP Chip



MassARRAY™

Compact System

Affymetix SNP Chip

ABI 7900



Pharmacogenomics

The effects of an individual’s genotype on thepharmacokinetics and pharmacodynamics ofdrug action.





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Gefitinib (Iressa)



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



Gefitinib•25/275 patients at Mass General identified as being responsive. EGFR sequenced in 9

responsive patients.

f b



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).



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.



Warfarin (Coumadin)

W f i



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



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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• 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

Documents

Introduction to Pharmacogenomics