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

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

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

1. chemical-genetic interaction profiles

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

ERG11Fluconazole

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

CNB1

P = 3.8 X 10-

56

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

Dead Alive

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?