1. Integration of chemical-genetic & genetic interaction data links bioactive compounds to cellular target pathways Parsons et al. 2004 Nature Biotechnology Jed Shimizu Medical Genetics 505 March 31, 2005

2. The Goal: Identifying targets of possible drugs Gene A Bioactive compound

3. The Method: Using the S. cerevisiae deletion set ~5000 non-essential genes in yeast make up library of viable mutants Synthetic Lethality: Gene YGene A

4. The Method: Using the S. cerevisiae deletion set ~5000 non-essential genes in yeast make up viable mutant set Synthetic Lethality: Gene Y deletion Alive

5. The Method: Using the S. cerevisiae deletion set ~5000 non-essential genes in yeast make up viable mutant set Synthetic Lethality: Alive Gene A deletion Alive

6. The Method: Using the S. cerevisiae deletion set ~5000 non-essential genes in yeast make up viable mutant set Synthetic Lethality: Alive Genes A & Y deletion Dead

7. Synthetic Lethal Interaction Means… redundant function interact with each other mediate other’s function Dead

8. Gene A? Screen Deletion Set with Drug of Interest Chemical-Genetic Interaction Profile

9. Back to Synthetic Lethality and the deletion set… Create collection of synthetic lethality profiles for possible drug target genes Genetic Interaction Profiles

10. Then Compare… …and find gene target of drug

11. Summary of Paper Parsons et al. establish proof of concept: 1.chemical-genetic interaction profiles for 12 known inhibitory drugs 2.clean up noise in above profiles 3.genetic interaction profiles of possible gene targets 4.compare (1) and (3)

12. Genetic Array Analysis:

13. 1. chemical-genetic interaction profiles

15. Address Accuracy- Rapamycin Array contained 85 published rapamycin- sensitive strains Found 246 rapamycin-sensitive strains in total 39 of these among previously published Confirmed another 22 by spot assay

16. 2. clean up the noise Found genes with sensitivity to multiple drugs: A multidrug-resistant gene set Included genes for: ergosterol biosynthesis – membrane fluidity vacuolar protein sorting vacuolar H-ATPase complex

17. 2. clean up the noise

18. 3. genetic interaction profiles- ERG11 example ERG11 Fluconazole

19. 3. genetic interaction profiles- ERG11 example

20. Interaction profiles overlapped for 13 genes ERG11 genetic profile identified 14 genes Fluconazole profile identified 62 genes

21. 3. genetic interaction profiles- ERG11 example Interaction profiles overlapped for 11 genes ERG11 genetic profile identified 14 genes Fluconazole profile identified 35 genes

22. 3. genetic interaction profiles- CNB1 example

24. 3. genetic interaction profiles - Significance ERG11 CNB1 P = 3.8 X 10 -56 P = 4.4 X 10 -53 P = 2.7 X 10 -60

25. 3. genetic interaction profiles – Why the Discrepancy? Difference between chemical and genetic interactions Genetic- no gene products Chemical- act on gene product DeadAlive Gene Y Gene Y associated to drug sensitivity due to interaction with drug, not drug target Drug

26. 4. comparison of interaction profiles Focused on 6 Drugs Compiled genetic interaction profiles for gene encoding drug target & related genes (57 in total) Filtered multidrug-resistance set

27. 4. comparison of interaction profiles

28. 4. comparison of interaction profiles – Bonus Info Provide info on uncharacterized genes: VID21- sensitive to camptothecin and hydroxyurea, possible role in DNA damage response

29. Chemical-Genetic Interaction Profile Genetic Interaction Profiles A Useful System to find Drug Targets? get a lot of information may work for certain drugs better finding precise target difficult

30. Will become increasingly useful… growing compendium of genetic profiles groups already systematically compiling genetic interaction data using synthetic gene analysis in worms, flies, mammalian cell lines

31. Questions or Thoughts?