Present day approaches to uncover gene function often rely on the ability to construct gene knockouts. While this gene-by-gene approach is straightforward in organisms with facile genetic methods such as yeast and flies, it is difficult in most other organisms. Furthermore, gene knockouts only allow analysis of nonessential genes. Fast acting, reversible chemical probes are an ideal way to perturb the function of essential genes. The primary objective of this proposal is to identify inhibitory chemical probes for all essential gene products in yeast using a genome-wide method that allows us to profile the relative sensitivity all protein targets in a cell simultaneously. This chemogenomic assay, Haplolnsufficiency Profiling (HIP), is based on the observation that lowering the dosage of a single gene from two copies to one copy in diploid yeast results in a heterozygote that is sensitized to any compound that acts on the product of this gene (Nat Genet. 21,278 (1999)). In the assay, a complete collection of 5,918 heterozygous deletion strains is pooled, grown competitively in the presence of compound and sampled. Molecular bar-codes incorporated into each strain allow parallel analysis and relative strain fitness to be quantitatively assessed by hybridization to oligonucleotide arrays. We validated the assay by screening 1,200 compounds with known biological activity. For all FDA therapeutics screened, the strain heterozygous for the known target was highly sensitive to drug. Recent breakthroughs in assay miniaturization and automation enable high-throughput screening of large numbers of compounds. As a result, the assay can now be implemented in a combined functional genomics and compound discovery effort. The outcome of this effort will be a catalog of chemical probes and their essential gene targets. In addition, such genome-wide exploration of biological and chemical space will identify novel, """"""""druggable"""""""" targets and allow characterization of chemical structures that comprise """"""""drug-like"""""""" compounds. As part of this effort, data will be disseminated to the community via a web interface. ? ?

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG003317-03
Application #
7117369
Study Section
Genome Study Section (GNM)
Program Officer
Ozenberger, Bradley
Project Start
2004-09-15
Project End
2008-08-31
Budget Start
2006-09-01
Budget End
2007-08-31
Support Year
3
Fiscal Year
2006
Total Cost
$976,497
Indirect Cost
Name
Stanford University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305
Aiyar, Raeka S; Bohnert, Maria; Duvezin-Caubet, Stéphane et al. (2014) Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders. Nat Commun 5:5585
Nile, Aaron H; Tripathi, Ashutosh; Yuan, Peihua et al. (2014) PITPs as targets for selectively interfering with phosphoinositide signaling in cells. Nat Chem Biol 10:76-84
Schlecht, Ulrich; Suresh, Sundari; Xu, Weihong et al. (2014) A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system. BMC Genomics 15:263
Cokol, Murat; Weinstein, Zohar B; Yilancioglu, Kaan et al. (2014) Large-scale identification and analysis of suppressive drug interactions. Chem Biol 21:541-551
Lee, Anna Y; St Onge, Robert P; Proctor, Michael J et al. (2014) Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science 344:208-11
Kittanakom, Saranya; Arnoldo, Anthony; Brown, Kevin R et al. (2013) Miniature short hairpin RNA screens to characterize antiproliferative drugs. G3 (Bethesda) 3:1375-87
St Onge, Robert; Schlecht, Ulrich; Scharfe, Curt et al. (2012) Forward chemical genetics in yeast for discovery of chemical probes targeting metabolism. Molecules 17:13098-115
Wu, Manhong; Zheng, Ming; Zhang, Weiruo et al. (2012) Identification of drug targets by chemogenomic and metabolomic profiling in yeast. Pharmacogenet Genomics 22:877-86
Douglas, Alison C; Smith, Andrew M; Sharifpoor, Sara et al. (2012) Functional analysis with a barcoder yeast gene overexpression system. G3 (Bethesda) 2:1279-89
Blackman, Ronald K; Cheung-Ong, Kahlin; Gebbia, Marinella et al. (2012) Mitochondrial electron transport is the cellular target of the oncology drug elesclomol. PLoS One 7:e29798

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