Cancer Pharmacogenetics: Lessons Learned

1. Cancer Pharmacogenetics: Lessons Learned Geoffrey Liu, MD FRCPC Scientist, OCI

2. Currently Approved Oncology Drugs

3. Cost of Colorectal Cancer Treatment Per 6 Months ($) Meropol NJ, Schulman KA. Cost of Cancer Care: Issues and Implications. J Clin Oncol 2007 25:180-186.

4. NY Times, September 2, 2009

5. Personalized Medicine Tailoring medical prevention and treatment therapies to the characteristics of each patient improving their quality of life and health outcome. "The right medicine to the right person at the right dosage at the right time" Pharmacoepidemiology Pharmacogenomics

6. "Here's my sequence...” New Yorker

7. Personalized or Predictive Medicine Respondto treatment Patients with same diagnosis No responseto treatment Experienceadverse events

8. What Disciplines are Involved? Personalized/Stratified/Predictive Medicine Pharmaco- epidemiology Molecularbiology Bioethics Bioinformatics BioStatistics Genomics Pharmacology

9. Cancer Pharmacogenomics (PGx) • The study of how variation in an individual’s germline and/or tumor genome are related to their metabolism and physiological response to drugs used in cancer treatment • Single Nucleotide Polymorphisms (substitutions) • Insertions and deletions • Copy number Variations • Methylation patterns • Molecular biomarkers • Gene expression

10. Cancer Pharmacogenetics Cancer Pharmacogenomics Biomarkers Predictive for Drug Outcomes Biomarkers Predictive for Treatment Outcomes

11. Cancer Pharmacogenetics GERMLINE Cancer Pharmacogenomics SOMATIC or TUMOUR Biomarkers Predictive for Drug Outcomes PROTEINS, IMAGING Biomarkers Predictive for Treatment Outcomes RADIATION THERAPY

12. Gene Mutations — Inherited or Acquired Hereditary (germline) mutations alterations in DNA inherited from a parent and are found in the DNA of virtually all of your cells. Acquired (somatic) mutations alterations in DNA that develop throughout a person’s life

13. Somatic Examples • Her2neu and Herceptin in breast ca • KRAS and EGFR MoAbs in colorectal ca • EGFR activating mutations and EGFR TKIs in NSCLC • ?ALK-EML4 translocation and ALK-targeting • ?BRAF mutations and BRAF inhibitor in melanoma

14. (inherited) Genetic Variations? Gene and Protein Expression Levels/Function/Regulation Substitutions (or SNPs) Insertions Deletions Duplications Short repeats Gene deletions Copy Number Variation

15. Polymorphisms can alter function through multiple mechanisms Promoter Exon Intron UTRs Conformational change Binding site change Early termination

16. Polymorphisms can alter function through multiple mechanisms mRNA Transport guidance UTRs Promoter Exon Intron UTRs Regions that are spliced into non-coding RNAs “junk areas” microRNAs Meta-regulators

17. Pharmacodynamics (PD): the study of the biochemical and physiological effects of drugs and the mechanisms of drug action and the relationship between drug concentration and effect (Drug effect on the body) Pharmacokinetics (PK): the study of the time course of substances and their relationship with an organism or system (Journey of drugs) Absorption Distribution Metabolism Excretion Pharmacology Every aspect may affect the final drug effect

18. Pharmacogenetics • The Study of the genetics of factors related to PD and PK Genes involved in PK Drug Absorption/Transport Activation/Metabolism/Excretion Genes involved in PD Drug mechanism of action. targets/downstream effectors

19. High Level of Evidence Adapted from Coate et al, JCO, 2010)

20. Candidate Genetic Factors Determining Drug Response • Polymorphisms in • Drug Receptors/Targets • Beta-2AR • Drug Transporters • MDR1 • Drug Metabolizing Enzymes • CYP2D6

21. Goal of Pharmacogenetics Optimize Therapy So Benefits Outweigh the Risks

22. Methodological Approaches • Biological Pathway-defined • Epidemiological Association Studies • In vitro and In vivo • Human tissue and Clinical Information

23. Issues to consider with Epidemiological Association Studies • Tumour vs Blood = which is your target tissue? • When do you believe an association study biomarker result? • Multiple comparisons? • Heterogeneity (of disease, of patients, of clinical scenario) = humans are not mice; how are these things controlled? • Biological Grounding/Functional Data? • Study Design and Study Population issues = if I choose the “right” controls, I will always be able to find a statistically significant result

24. Three Common Genetic and Epidemiological Approaches • Germline • Candidate-Gene • Genome-Wide Association (GWAS) • Candidate-Pathway

25. Candidate-Gene Approach Typically genetic variants are selected based on their known physiologic or pharmacologic effect on disease or drug response

26. Three Cancer Examplesof candidate polymorphism approaches • Irinotecan and UGT1A1 polymorphisms • Tamoxifen and CYP2D6 polymorphisms • EGFR tyrosine kinase inhibitors and EGFR polymorphisms

27. Three Cancer Examplesof candidate polymorphism approaches • Irinotecan and UGT1A1 polymorphisms • Tamoxifen and CYP2D6 polymorphisms • EGFR tyrosine kinase inhibitors and EGFR polymorphisms EACH TO ILLUSTRATE SPECIFIC ISSUES WITH ASSOCIATION STUDIES

28. SN-38+Glucuronide Irinotecan metabolism and its toxicity ATP-binding cassette transporters (ABC gene family) Help drug transfer into hepatic cell membrane carboxylesterase 1, 2 Cytochrome P450 3Afamily Bone Marrow Intestine Leukopenia Thrombocytopenia Anemia Diarrhea (UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily

29. SN-38+Glucuronide Irinotecan metabolism and its toxicity ATP-binding cassette transporters (ABC gene family) Help drug transfer into hepatic cell membrane carboxylesterase 1, 2 Cytochrome P450 3Afamily Bone Marrow Intestine Leukopenia Thrombocytopenia Anemia Diarrhea (UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily

30. SN-38+Glucuronide Irinotecan metabolism and its toxicity ATP-binding cassette transporters (ABC gene family) Help drug transfer into hepatic cell membrane carboxylesterase 1, 2 Cytochrome P450 3Afamily Bone Marrow Intestine Leukopenia Thrombocytopenia Anemia Diarrhea (UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily

31. SN-38+Glucuronide Irinotecan metabolism and its toxicity ATP-binding cassette transporters (ABC gene family) Help drug transfer into hepatic cell membrane carboxylesterase 1, 2 Cytochrome P450 3Afamily Bone Marrow Intestine Leukopenia Thrombocytopenia Anemia Diarrhea (UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily

32. SN-38+Glucuronide Irinotecan metabolism and its toxicity ATP-binding cassette transporters (ABC gene family) Help drug transfer into hepatic cell membrane carboxylesterase 1, 2 Cytochrome P450 3Afamily Bone Marrow Intestine Leukopenia Thrombocytopenia Anemia Diarrhea (UGT1A)-- uridine diphospho-glucuronosyltransferase 1A subfamily

33. UGT1A1 Genotype Innocenti et al, JCO, 2004

34. UGT1A1 Genotype Less functional allele

35. UGT1A1 Genotype Less functional allele

36. 28AA ~243 AA ~269AA Signal peptide Functional part Protein structure of UGT1A family 540 AA, 28 signal AA, ~243 common AA in different isoforms C N

37. 28AA ~243 AA ~269AA Signal peptide Functional part Protein structure of UGT1A family 540 AA, 28 signal AA, ~243 common AA in different isoforms TM

38. 28AA ~243 AA ~269AA Signal peptide Functional part Protein structure of UGT1A family 540 AA, 28 signal AA, ~243 common AA in different isoforms

39. UGT1A gene family: Alternative Splicing Variants

40. Important Genetic Variations for UGT1A1

41. UGT1A7 allele nomenclature and important SNPs

42. UGT1A9 allele nomenclature and important SNPs

43. Chr2:234330521-Chr2:234330398 =123bp Chr234333883-Chr23433633 =250bp UGT1A1 2 3 4 5A 5B UGT1A1*6 rs4148323 UGT1A1*28 rs8175347 UGT1A1*93 -3156G>A rs10929302 UGT1A1*60 -3279T>G rs4124874 Variations across UGT1A polymorphisms Chr234255266-Chr234255944 =678bp Chr2, 234245202 UGT1A7 UGT1A9 -57 T>G rs7586110 622T>C W208R rs176832 391C>A(rs17863778), 392G>A(rs17868324) R131K 342 G>A G115S() 387T>G N129K rs176832 UGT1A9*22 -118T9/T10 rs3832043 UGT1A7 *1*2*3*4*5*6*7*8*9*10*11*12*14

44. Current Situation • UGT1As much more complex than initially thought • Additional polymorphisms involved in determining metabolism of irinotecan • Despite FDA labeling change, UGT testing is currently not being used widespread.

45. Current Situation • UGT1As much more complex than initially thought • Additional polymorphisms involved in determining metabolism of irinotecan • Despite FDA labeling change, UGT testing is currently not being used widespread. CLINICAL UTILITY?

46. Take-Home Message:Heterogeneity and Complexity of Associations affect Results That is why you get difference association studies that state that red meat is good, neutral or bad for you….

47. …but don’t throw the baby out with the bathwater

48. Training-Test Paradigmin Human Samples • Training Set (correct for multiple comparisons) • Multiple Validation Sets

49. Causal Prognostic Factors Biomarkers related to the host Environmental Modifying Factors Psychosocial Cultural, Economic Treatment Factors Biomarkers of tumor • Clinical Outcomes • Hard outcomes (OS/DFS) • Soft outcomes (toxicity/QOL) Non-causal Prognostic Factors Adapted from Liu et al, 2006 From Bench to Bedside:Complexity of the Human Being

50. Causal Prognostic Factors Biomarkers related to the host Environmental Modifying Factors Psychosocial Cultural, Economic Treatment Factors Biomarkers of tumor • Clinical Outcomes • Hard outcomes (OS/DFS) • Soft outcomes (toxicity/QOL) Non-causal Prognostic Factors Adapted from Liu et al, 2006 From Bench to Bedside:Complexity of the Human Being Pharmacogenetics