Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways

Abstract

Bioactive compounds can be valuable research tools and drug leads, but it is often difficult to identify their mechanism of action or cellular target. Here we investigate the potential for integration of chemical-genetic and genetic interaction data to reveal information about the pathways and targets of inhibitory compounds. Taking advantage of the existing complete set of yeast haploid deletion mutants, we generated drug-hypersensitivity (chemical-genetic) profiles for 12 compounds. In addition to a set of compound-specific interactions, the chemical-genetic profiles identified a large group of genes required for multidrug resistance. In particular, yeast mutants lacking a functional vacuolar H(+)-ATPase show multidrug sensitivity, a phenomenon that may be conserved in mammalian cells. By filtering chemical-genetic profiles for the multidrug-resistant genes and then clustering the compound-specific profiles with a compendium of large-scale genetic interaction profiles, we were able to identify target pathways or proteins. This method thus provides a powerful means for inferring mechanism of action.

Budding YeastSSD1-VRegulates Transcript Levels of Many Longevity Genes and Extends Chronological Life Span in Purified Quiescent Cells

“…These genes show a striking enrichment (Hong et al, 2008) for posttranslational modifiers (p ϭ 10 Ϫ14 ), including 19 kinases and nine histone deacetylases, and genes involved in the cell cycle and cell morphogenesis (p ϭ 10 Ϫ8 ). ssd1 mutants display sensitivity to high osmolarity, caffeine, fungicides¤ and numerous other compounds, which suggests a role for this protein in the maintenance of cell wall integrity (Ibeas et al, 2001;Parsons et al, 2004), but its mechanism of action remains obscure.…”

“…These genes show a striking enrichment (Hong et al, 2008) for posttranslational modifiers (p ϭ 10 Ϫ14 ), including 19 kinases and nine histone deacetylases, and genes involved in the cell cycle and cell morphogenesis (p ϭ 10 Ϫ8 ). ssd1 mutants display sensitivity to high osmolarity, caffeine, fungicides¤ and numerous other compounds, which suggests a role for this protein in the maintenance of cell wall integrity (Ibeas et al, 2001;Parsons et al, 2004), but its mechanism of action remains obscure.Despite, or perhaps because of, its impact on so many different cellular functions, SSD1 is a common site of variation in both laboratory strains and natural populations of budding yeast (Wheeler et al, 2003). One possible explanation is that SSD1-V, which encodes the full-length "wildtype" protein, reduces the virulence of Saccharomyces cerevisiae in one mouse model (Wheeler et al, 2003), but SSD1-V is critical in Candida (Gank et al, 2008) and several fungal pathogens of plants for evading their hosts' defense systems (Tanaka et al, 2007).…”

Match-making for posaconazole through systems thinking

“…While the bulk of experimental evidence comes from high throughput screens and needs to be treated with caution, there is solid support for synthetic lethality between ELO3 and ERG6 [5], and for synthetic growth defects of sterol synthetic genes with ISC1, SUR2, and SCS7 [4]. Strikingly, synthetic lethality has been demonstrated between CYP51 and SCS7 [31].…”

Reference profiling of the genomic response induced by an antimicrotubule agent, TZT-1027 (Soblidotin), in vitro

“…18,19 Cell-based high-throughput screening technologies provide information about cellular pathways that control drug sensitivity. 20,21 Drug-to-drug comparative approaches using microarray analyses are useful for identifying drug targets; the cellular effects caused by a novel drug of incompletely characterized specificity can be matched to 'reference profiles' of the cellular effects elicited by the specific inhibition of candidate analog-sensitive drugs. 22,23 Thus, it has been proposed that phenotypic information generated by drug-induced alterations in gene expression can be matched to discrete interactions between the compound and the relevant protein targets.…”