Transcript Genetic Interaction Profiles

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
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
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:
Gene A deletion
Alive
Alive
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
Synthetic Lethal Interaction Means…
Dead
•redundant function
•interact with each other
•mediate other’s function
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
1. chemical-genetic interaction profiles
1. chemical-genetic interaction profiles
Address Accuracy- Rapamycin
Array contained 85 published rapamycinsensitive 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
Fluconazole
ERG11
3. genetic interaction profiles- ERG11 example
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- CNB1 example
3. genetic interaction profiles - Significance
ERG11
P = 3.8 X 10-56
CNB1
P = 4.4 X 10-53
P = 2.7 X 10-60
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
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
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
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?