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=== Project Descriptions === '''''High-throughput identification of human drug targets in Saccharomyces cerevisiae''''' The development of drug-based therapies has been a mainstay of biomedical research for the past 50 years. With the dawn of the “omics” era, the discovery rate of novel drugs, therapeutic targets and related biochemical pathways has the potential to increase significantly. However, we have not yet seen a dramatic increase in the number of novel drugs. The emergent discipline of chemogenomics has developed to determine genome-wide organismal changes in response to treatment with chemical compounds and may help alleviate the current drug bottleneck. In our assay, we transform the yeast Saccharomyces cerevisiae with the entire human ORFeome collection (approximately 12000 ORFs), generating a collection of yeast in which each strain should overexpress a single human protein upon induction. The collection was subsequently pooled and treated with a drug at growth inhibitory concentrations, such that only strains that are resistant can survive and reproduce. We have termed this assay as human Transgene Overexpression in Yeast (TOY). After drug treatment, ORFs are extracted, amplified and hybridized onto a human gene microarray as a readout of relative ORFs abundance. Human genes (the ORFs) that confer resistance to the drug challenge when overexpressed are assumed to either (a) directly interact with the compound or (b) buffer an orthologous pathway that interacts with the compound. As a proof-of-principle, human TOY was used to successfully identify dihydrofolate reductase (DHFR) as a drug target of the folate biosynthesis inhibitor methotrexate. Additional potential human drug targets of methotrexate were also identified, warranting further investigation. In a separate analysis, the pool was treated with clozapine, an antipsychotic drug used to treat drug-resistant schizophrenia. This screen yielded multiple potential targets, several of which were linked to schizophrenia in the literature. Therefore, the human TOY assay can be used to determine potential drug targets and off-target effects. As more ORFs are being added to the human ORFeome (current predicted max of ~24000), chemogenomic profiles will be expanded. The genome-wide portraits of drug action determined using this assay may aid in increasing the rate of drug discovery and characterization. '''''Enriching for drug-gene interactions in genome-wide screens''''' Project description coming soon |
Ron Ammar
Ron is a PhD candidate in the Bader/Giaever/Nislow labs. His research seeks to answer biological questions through the integration of bioinformatic and high-throughput large scale molecular methods.
Project Descriptions
High-throughput identification of human drug targets in Saccharomyces cerevisiae
The development of drug-based therapies has been a mainstay of biomedical research for the past 50 years. With the dawn of the “omics” era, the discovery rate of novel drugs, therapeutic targets and related biochemical pathways has the potential to increase significantly. However, we have not yet seen a dramatic increase in the number of novel drugs. The emergent discipline of chemogenomics has developed to determine genome-wide organismal changes in response to treatment with chemical compounds and may help alleviate the current drug bottleneck. In our assay, we transform the yeast Saccharomyces cerevisiae with the entire human ORFeome collection (approximately 12000 ORFs), generating a collection of yeast in which each strain should overexpress a single human protein upon induction. The collection was subsequently pooled and treated with a drug at growth inhibitory concentrations, such that only strains that are resistant can survive and reproduce. We have termed this assay as human Transgene Overexpression in Yeast (TOY). After drug treatment, ORFs are extracted, amplified and hybridized onto a human gene microarray as a readout of relative ORFs abundance. Human genes (the ORFs) that confer resistance to the drug challenge when overexpressed are assumed to either (a) directly interact with the compound or (b) buffer an orthologous pathway that interacts with the compound. As a proof-of-principle, human TOY was used to successfully identify dihydrofolate reductase (DHFR) as a drug target of the folate biosynthesis inhibitor methotrexate. Additional potential human drug targets of methotrexate were also identified, warranting further investigation. In a separate analysis, the pool was treated with clozapine, an antipsychotic drug used to treat drug-resistant schizophrenia. This screen yielded multiple potential targets, several of which were linked to schizophrenia in the literature. Therefore, the human TOY assay can be used to determine potential drug targets and off-target effects. As more ORFs are being added to the human ORFeome (current predicted max of ~24000), chemogenomic profiles will be expanded. The genome-wide portraits of drug action determined using this assay may aid in increasing the rate of drug discovery and characterization.
Enriching for drug-gene interactions in genome-wide screens
Project description coming soon
Contact
Email: <ron DOT ammar AT utoronto DOT ca>
Other Affiliations
HIPHOP Lab Collaborative Graduate Program in Genome Biology and Bioinformatics
Department of Molecular Genetics, University of Toronto Terrence Donnelly Centre for Cellular and Biomolecular Research 160 College St, Rm 1240, Toronto ON, M5S 3E1, Canada Phone: 416-978-5067 Fax: 416-978-4842