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Integration of chemical-genetic & genetic interaction data links bioactive compounds to cellular target pathwaysParsons et al. 2004 Nature Biotechnology
Jed ShimizuMedical Genetics 505March 31, 2005
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The Goal:
Identifying targets of possible drugs
Gene A
Bioactive compound
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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
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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
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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
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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
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Synthetic Lethal Interaction Means…
•redundant function
•interact with each other
•mediate other’s function
Dead
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Gene A?
Screen Deletion Set with Drug of Interest
Chemical-Genetic Interaction Profile
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Back to Synthetic Lethality and the deletion set…
Create collection of synthetic lethality profiles for possible drug target genes
Genetic Interaction
Profiles
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Then Compare…
…and find gene target of drug
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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)
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Genetic Array Analysis:
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1. chemical-genetic interaction profiles
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1. chemical-genetic interaction profiles
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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
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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
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2. clean up the noise
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3. genetic interaction profiles- ERG11 example
ERG11Fluconazole
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3. genetic interaction profiles- ERG11 example
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3. genetic interaction profiles- ERG11 example
Interaction profiles overlapped for 13 genes
ERG11 genetic profile identified 14 genes
Fluconazole profile identified 62 genes
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3. genetic interaction profiles- ERG11 example
Interaction profiles overlapped for 11 genes
ERG11 genetic profile identified 14 genes
Fluconazole profile identified 35 genes
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3. genetic interaction profiles- CNB1 example
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3. genetic interaction profiles- CNB1 example
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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
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3. genetic interaction profiles – Why the Discrepancy?Difference between chemical and genetic interactions
•Genetic- no gene products
•Chemical- act on gene product
Dead Alive
Gene Y
Gene Y associated to drug sensitivity due to interaction with drug, not drug target
Drug
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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
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4. comparison of interaction profiles
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4. comparison of interaction profiles – Bonus Info
Provide info on uncharacterized genes:
VID21- sensitive to camptothecin and hydroxyurea, possible role in DNA damage response
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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
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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
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Questions or Thoughts?