Genes and Drugs

1. Genes and Drugs

2. 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

3. How do we know if a patient will respond (or have an adverse response) to a drug? (we don’t)

4. 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

5. Some examples of drug response rates

6. 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

7. 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

8. 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

9. Potential causes of variability in drug effects: • Pathogenesis and the severity of the disease being treated. • Drug interactions from concomitant treatments (plasma protein binding, metabolism) • Individual’s age, gender, lifestyle (including environmental factors), behavior, nutritional state, renal and liver function, and concomitant illnesses. • Genetic variation

10. A patient’s response to a drug may depend on factors that can vary according to the alleles that an individual carries, including Pharmacokinetic factors • Absorption • Distribution • Metabolism • Elimination Pharmacodynamic factors • target proteins • downstream messengers

11. Phase I metabolism (oxidation by CYP450s)Over 1000 CYP450 enzymes identified (50 active enzymes in human). Expressed mainly in liver. Multiple alleles with different frequencies in different ethnic groups P450 enzymes oxidize drugs or other xenobiotics in order to: 1. increase polarity, and enhance excretion (decrease resorption in distal nephron) 2. convert to substrate for phase2 metabolism RH + O2 + NADPH + H+ ROH +H2O +NADP+ CYP450

12. CYP450s important in Drug Metabolism CYP3A4 • most important (50%) • inducible CYP2D6 • next in line (20%) • not inducible CYP2C9 and 2C19 • next (15%) • inducible * Functional allelic variants. There are 70 identified functional variants of CYP2D6 alone

13. Phase II metabolism (conjugation) Substrate is phase I reaction product, or other endogenous compound ( eg. steroid hormones) Congugaton of highly polar glucuronide enhances water solubility/decreases lipid solubility and thereby promotes excretion Fewer genes and functional variants than P450s Gtxase

14. EM Distribution of metabolic efficiency EM = extensive metabolizers PM = poor metabolizers PM Metabolic ratio = [parent]/[metabolite]

15. 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

16. Variation in the genome most relevant to pharmacogenomics: • Insertions/deletions (small and large) • Single nucleotide polymorphisms (SNPs)

17. gains losses Copy Number Polymorphisms in Human Genome • 39 healthy unrelated individuals • 255 loci • 24 variants present in >10% of individuals • Iafrate et al., Nat Genet. 36, 949 (2004)

19. SNPs are the most commonly occurring genetic differencesACGCCTTGACGAAGCTTAC ACGCCTTGACGATGCTTACSNPs are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist wherein the least frequent allele has an abundance of 1% or greater

20. SNPs are estimated to occur throughout the genome 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 present in pop’n at large • There are expected to be a total of 10-20M SNPs in human population

21. Biochemistryof SNP Genotyping

22. MassARRAY™ Compact System AffymetixSNP Chip ABI 7900

23. Pharmacogenomics The effects of an individual’s genotype on the pharmacokinetics and pharmacodynamics of drug action.

25. 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

26. Gefitinib (Iressa)

27. Gefitinib • Epidermal Growth Factor Receptor over-expressed in 40-80% of Non-Small-Cell Lung 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

28. 25/275 patients at Mass General identified as being responsive. EGFR sequenced in 9 responsive patients. Gefitinib

29. 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).

30. 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.

31. Warfarin (Coumadin)

32. 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

33. genetic factors influencing warfarin response unknown. • genetic data may help determining correct dose and preventing adverse reactions • present study: type 14 genes in 1000+ patients and associate variants with warfarin response Warfarin

34. 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

35. 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