title: A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells.
abstract: Small molecules often affect multiple targets, elicit off-target effects, and induce genotype-specific responses. Chemical genetics, the mapping of the genotype dependence of a small molecule's effects across a broad spectrum of phenotypes can identify novel mechanisms of action. It can also reveal unanticipated effects and could thereby reduce high attrition rates of small molecule development pipelines. Here, we used high-content screening and image analysis to measure effects of 1,280 pharmacologically active compounds on complex phenotypes in isogenic cancer cell lines which harbor activating or inactivating mutations in key oncogenic signaling pathways. Using multiparametric chemical-genetic interaction analysis, we observed phenotypic gene-drug interactions for more than 193 compounds, with many affecting phenotypes other than cell growth. We created a resource termed the Pharmacogenetic Phenome Compendium (PGPC), which enables exploration of drug mode of action, detection of potential off-target effects, and the generation of hypotheses on drug combinations and synergism. For example, we demonstrate that MEK inhibitors amplify the viability effect of the clinically used anti-alcoholism drug disulfiram and show that the EGFR inhibitor tyrphostin AG555 has off-target activity on the proteasome. Taken together, this study demonstrates how combining multiparametric phenotyping in different genetic backgrounds can be used to predict additional mechanisms of action and to reposition clinically used drugs.
authors.affiliation: Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany Department of Cell and Molecular Biology, Heidelberg University, Heidelberg, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Breinig
authors.affiliation: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
authors.forename: Felix A
authors.initials: FA
authors.lastname: Klein
authors.affiliation: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany whuber@embl.de m.boutros@dkfz.de.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Huber
authors.affiliation: Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany Department of Cell and Molecular Biology, Heidelberg University, Heidelberg, Germany whuber@embl.de m.boutros@dkfz.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Boutros
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology*; D049109:Cell Proliferation / Q000187:drug effects; D002470:Cell Survival / Q000187:drug effects; D015870:Gene Expression / Q000187:drug effects; D045325:HCT116 Cells; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D057054:Molecular Imaging / Q000379:methods*; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D015398:Signal Transduction
chemical_list: D000970:Antineoplastic Agents
keywords: compound mode of action; drug synergism; high‐content imaging; isogenic cell lines; systems pharmacology