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The Goal:

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

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The Goal:

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  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 A Gene Y

  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: Gene A deletion Alive Alive

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

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

  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: • chemical-genetic interaction profiles for 12 known inhibitory drugs • clean up noise in above profiles • genetic interaction profiles of possible gene targets • compare (1) and (3)

  12. Genetic Array Analysis:

  13. 1. chemical-genetic interaction profiles

  14. 1. chemical-genetic interaction profiles

  15. 1. chemical-genetic interaction profiles 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- ERG11example

  20. 3. genetic interaction profiles- ERG11example Interaction profiles overlapped for 13 genes ERG11 genetic profile identified 14 genes Fluconazole profile identified 62 genes

  21. 3. genetic interaction profiles- ERG11example Interaction profiles overlapped for 11 genes ERG11 genetic profile identified 14 genes Fluconazole profile identified 35 genes

  22. 3. genetic interaction profiles- CNB1 example

  23. 3. genetic interaction profiles- CNB1 example

  24. 3. genetic interaction profiles - Significance ERG11 P = 3.8 X 10-56 P = 4.4 X 10-53 CNB1 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 Drug Gene Y Dead Alive Gene Y associated to drug sensitivity due to interaction with drug, not drug target

  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. A Useful System to find Drug Targets? Chemical-Genetic Interaction Profile Genetic Interaction Profiles • 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?

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