title: Linking phenotypes and modes of action through high-content screen fingerprints.
abstract: High-content screening (HCS) is a powerful technique for monitoring phenotypic responses to treatments on a cellular and subcellular level. Cellular phenotypes can be characterized by multivariate image readouts such as shape, intensity, or texture. The corresponding feature vectors can thus be defined as HCS fingerprints that serve as a powerful biological compound descriptor. Therefore, clustering or classification of HCS fingerprints across compound treatments allows for the identification of similarities in protein targets or pathways. We developed an HCS-based profiling panel that serves as basis for characterizing the mode of action of compounds. This panel measures phenotypic effects in six different compartments of U-2OS cells, namely the nucleus, the cytoplasm, the endoplasmic reticulum, the Golgi apparatus, and the cytoskeleton. We profiled a set of 2,725 well-annotated compounds and clustered their corresponding HCS fingerprints to establish links between predominant cellular phenotypes and cellular processes and protein targets. We found various different clusters enriched for individual targets (e.g., HDAC, HSP90, TOP1, HMGCR, TUB), signaling pathways (e.g., PIK3/AKT/mTOR), or gene sets associated with diseases (e.g., psoriasis, leukemia). Based on this clustering we were able to identify novel compound-target associations for selected compounds such as a submicromolar inhibitory activity of Silmitasertib (a casein kinase inhibitor) on PI3K and mTOR.
authors.affiliation: Novartis Institutes for BioMedical Research , Center for Proteomic Chemistry, Basel, Switzerland .
authors.forename: Felix
authors.initials: F
authors.lastname: Reisen
authors.affiliation: Novartis Institutes for BioMedical Research , Center for Proteomic Chemistry, Basel, Switzerland .
authors.forename: Amelie
authors.initials: A
authors.lastname: Sauty de Chalon
authors.affiliation: Novartis Institutes for BioMedical Research , Center for Proteomic Chemistry, Basel, Switzerland .
authors.forename: Martin
authors.initials: M
authors.lastname: Pfeifer
authors.affiliation: Novartis Institutes for BioMedical Research , Center for Proteomic Chemistry, Basel, Switzerland .
authors.forename: Xian
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Novartis Institutes for BioMedical Research , Center for Proteomic Chemistry, Basel, Switzerland .
authors.forename: Daniela
authors.initials: D
authors.lastname: Gabriel
authors.affiliation: Novartis Institutes for BioMedical Research , Center for Proteomic Chemistry, Basel, Switzerland .
authors.forename: Paul
authors.initials: P
authors.lastname: Selzer
mesh_terms: D057166:High-Throughput Screening Assays / Q000379:methods*; D056572:Histone Deacetylase Inhibitors / Q000494:pharmacology; D006801:Humans; D010641:Phenotype; D000081082:Phosphoinositide-3 Kinase Inhibitors; D058570:TOR Serine-Threonine Kinases / Q000037:antagonists & inhibitors; D050257:Tubulin Modulators / Q000494:pharmacology
chemical_list: D056572:Histone Deacetylase Inhibitors; D000081082:Phosphoinositide-3 Kinase Inhibitors; D050257:Tubulin Modulators; D058570:TOR Serine-Threonine Kinases