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

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

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

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

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

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

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

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

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

Then Compare… …and find gene target of drug

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)

Genetic Array Analysis:

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

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

2. clean up the noise

3. genetic interaction profiles- ERG11 example ERG11 Fluconazole

3. genetic interaction profiles- ERG11 example

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

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

3. genetic interaction profiles- CNB1 example

3. genetic interaction profiles - Significance ERG11 CNB1 P = 3.8 X P = 4.4 X P = 2.7 X

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

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

4. comparison of interaction profiles

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

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

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

Questions or Thoughts?