Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action

“For example, one such approach [17] looks for similarities in gene expression profiles in response to the drug; whereas another [18] looks for similarities in side effects.”

“Functional prediction performance was compared using several types of functional yeast assays: co-fitness; a unified protein-protein interaction network [25] derived from two large-scale affinity precipitation studies [26,27]; synthetic lethality [28]; and co-expression over three microarray gene expression studies [2…”

“Functional prediction performance was compared using several types of functional yeast assays: co-fitness; a unified protein-protein interaction network [25] derived from two large-scale affinity precipitation studies [26,27]; synthetic lethality [28]; and co-expression over three microarray gene expression studies […”

“Phenotype in rich medium (one feature) In the absence of drug, if the homozygous deletion strain gi initially showed no phenotype relative to wild type [9,78], the target cannot be identified by the heterozygous deletion assay as this assay is dependent on diminished 'functional dosage' of the drug target based on gro…”

“coli and used to transform the BY4743 wild-type strain (MATa/α his3Δ 1/ his3Δ 1 leu2Δ 0/leu2Δ 0 lys2Δ 0/LYS2 MET15/met15Δ 0 ura3Δ 0/ura3Δ 0) lacking the KanMX-marker [71].”

“Functional prediction performance was compared using several types of functional yeast assays: co-fitness; a unified protein-protein interaction network [25] derived from two large-scale affinity precipitation studies [26,27]; synthetic lethality [28]; and co-expression over three microarray gene expression studies [2…”

“Functional prediction performance was compared using several types of functional yeast assays: co-fitness; a unified protein-protein interaction network [25] derived from two large-scale affinity precipitation studies [26,27]; synthetic lethality [28]; and co-expression over three microarray gene expression studies [2…”

“For example, one class of methods [19,20] searches for similarity of RNA expression profiles after drug exposure to profiles resulting from a conditional or complete gene deletion.”

“Functional prediction performance was compared using several types of functional yeast assays: co-fitness; a unified protein-protein interaction network [25] derived from two large-scale affinity precipitation studies [26,27]; synthetic lethality [28]; and co-expression over three microarray gene expression studies [2…”

“The success of these methods to date has been variable, with some studies able to predict known interactions with significant enrichment, and others performing worse than random [55-57].”

“Nystatin is known to bind to membrane ergosterol, and it causes cell death by creating pores in the plasma membrane [50].”

“In an initial test we found that paralogous (duplicated) gene pairs [34] tend to exhibit higher-than-average co-fitness values (t-test P < 0.”

“Detailed biochemical characterization will be required to elucidate the exact nature of this interaction which, based on renewed interest in clozapine [49], is of great medical value.”

“The fact that signal transduction is predicted relatively well by co-fitness, for example, may be explained by the fact that signal transduction is often a rapid response occurring on the order of milliseconds, a time frame too short to allow expression and translation of required proteins [53,54].”

“For example, one such approach [17] looks for similarities in gene expression profiles in response to the drug; whereas another [18] looks for similarities in side effects.”

“Traditionally, predictive methods rely on computationally intensive algorithms that involve molecular 'docking' [ 16 ] and require that the three-dimensional structure of the protein target be solved.”

“For example, some antifungal azole drugs such as miconazole inhibit several hundred strains, only one of which is deleted for the known target ERG11, (Figure 2) [1].”

“Classification of drug targets We applied several machine learning algorithms using the Weka packages [ 80 ]: Random Forest, Naive Bayes, Decision Stump, Logistic Regression, Support Vector Machine (SVM: SMO algorithm), Decision Tree (J48 algorithm), and Bayesian Network.”

“Our preliminary genetic data indicating a novel interaction between Cox17 and clozapine are tantalizing given the renewed interest in this drug [61], and deserve further investigation.”

“This finding can be attributed to structurally diverse compounds that inhibit different proteins within the same pathway, or to different compound structures that inhibit the same target [45,46].”

“Functional prediction performance was compared using several types of functional yeast assays: co-fitness; a unified protein-protein interaction network [25] derived from two large-scale affinity precipitation studies [26,27]; synthetic lethality [28]; and co-expression over three microarray gene expression studies [2…”

“Second, the 'rescuing protein' must be expressed at a level that can override the compound effect, but not expressed to a level that will inhibit yeast growth [48], which would therefore confound the detection of growth rescue.”

“A related approach employs gene-deletion fitness profiling, where the growth profiles of haploid deletion strains in the presence of drug are compared to growth profiles obtained in the presence of a second deletion [5].”

“Functional prediction performance was compared using several types of functional yeast assays: co-fitness; a unified protein-protein interaction network [25] derived from two large-scale affinity precipitation studies [26,27]; synthetic lethality [28]; and co-expression over three microarray gene expression studies [2…”

“Phenotype in rich medium (one feature) In the absence of drug, if the homozygous deletion strain gi initially showed no phenotype relative to wild type [9,78], the target cannot be identified by the heterozygous deletion assay as this assay is dependent on diminished 'functional dosage' of the drug target based on gro…”

“Regardless of the underlying reasons why co-fitness performs better for certain functions, this metric clearly provides distinct information that, when integrated with diverse data sources, will aid the development of tools designed to predict gene function [11,12].”

“This assay identifies genes required for growth in the presence of compound, often identifying functions that buffer the drug target pathway [5-8].”

“With this comprehensive analysis of the chemogenomic fitness assay results, we asked to what degree the assay could systematically predict drug targets [2-4].”

“COX17 overexpression To create the overexpression strains, yeast strain Y258 (MATa pep4-3, his4-580, ura 3-53, leu2-3,112 [81]) was transformed with plasmids BG1805 (Open Biosystems, Huntsville, AL, USA): the vector is derived from pRSAB1234 from Erin O'Shea using sequence verified, de novo synthesized yeast or human…”

“With this comprehensive analysis of the chemogenomic fitness assay results, we asked to what degree the assay could systematically predict drug targets [2-4].”

“Of these, 134 interactions were due to only two of the DrugBank compounds, staurosporine and emodin, which have many annotated human kinase targets, each of which had up to several BLASTp-determined homologs in yeast.”

“Kontoyiannis DP, Sagar N, Hirschi KD: Overexpression of Erg11p by the regulatable GAL1 promoter confers fluconazole resistance in Saccharomyces cerevisiae.”

“On average, 40% of an essential gene's significantly co-fit partners were also essential genes, compared to only 23% for non-essential gene's co-fit partners (P 37 ,38].”

“We calculated whether the set Ci was statistically enriched for any shared motif m, using a log risk ratio (RR), which has been applied in calculating other types of motif enrichment [79]:”

“Other computational methods utilize protein sequence rather than chemical structure, but these methods are only applicable to individual proteins or a small subset of proteins that possess a high degree of similarity [ 58-60 ].”

“Two more distance metrics were calculated across subsets of experiments, based on a biclustering analysis on the log2 ratios, using the BicAT toolbox [68] with the Iterative Signature Algorithm [69].”

“Two more distance metrics were calculated across subsets of experiments, based on a biclustering analysis on the log2 ratios, using the BicAT toolbox [68] with the Iterative Signature Algorithm [69].”

“Indeed, if we define a complex as essential if >80% of its members are essential, 68 of 312 complexes are essential in rich medium, which is significantly greater than that expected by chance [14].”

“The mammalian homolog is essential for development and participates in multiple biological processes, including vesicle targeting to the plasma membrane, protein translation, and filopodia extension [62,63].”

“Intuitively, if the protein is a bona fide target of the compound, decreasing gene dosage should increase sensitivity to compound (as in the HIP assay) by decreasing the amount of target protein, and increasing gene dosage should increase resistance to compound through overexpression of the target protein [21].”

“Other genes required for uncompromised growth in these antifungals include multi-drug resistance genes, such as the drug transporter PDR5 (the yeast homolog of human MDR1), the lipid transporter PDR16, and the transcription factor PDR1, which regulates both PDR5 and PDR16 expression [41].”

“The success of these methods to date has been variable, with some studies able to predict known interactions with significant enrichment, and others performing worse than random [55-57].”

“We first showed that, overall, co-fitness data identify gene function better than co-expression data but not as well as the physical interaction dataset when compared to a gold standard [13].”

“This rationale has been used with success in a study of 188 compounds [23].”

“This finding can be attributed to structurally diverse compounds that inhibit different proteins within the same pathway, or to different compound structures that inhibit the same target [ 45 ,46].”

“In this way, fitness data allow identification of the potential drug target [3,4,10].”

“This finding supports the hypothesis of partial, rather than strict, redundancy [35].”

“This COX alteration has been shown to be linked to clozapine's side effects [66,67].”

“Consistent with other recent studies [35, 36 ], our finding supports models that posit that such genes are partially redundant, with deletion of either duplicate resulting in a similar (that is, co-fit) phenotype.”

“Finally, over-expression profiling is an approach to drug target identification that relies on the concept that overexpression of a drug target should confer resistance to a compound [21-23].”

“Recent analyses [14,15] show that proteins that are essential in rich medium tend to cluster into complexes, suggesting that essentiality is, to a large extent, a property of the entire complex.”

“The mammalian homolog is essential for development and participates in multiple biological processes, including vesicle targeting to the plasma membrane, protein translation, and filopodia extension [62,63].”

“Yeast competitive fitness data constitute a unique, genome-wide assay of the cellular response to environmental and chemical perturbations [ 1-8 ].”

“Because their neurological targets do not exist in yeast, the sensitivity we observe is likely a result of these compounds affecting additional cellular targets in yeast [44]; these 'secondary' targets, if conserved, may correspond to additional targets of these compounds in human cells.”

“It is known that the microtubule-depolymerizer nocodazole distorts the filamentous localization of Exo84 in cultured mammalian cells [64].”

“For example, one class of methods [19,20] searches for similarity of RNA expression profiles after drug exposure to profiles resulting from a conditional or complete gene deletion.”

“Other computational methods utilize protein sequence rather than chemical structure, but these methods are only applicable to individual proteins or a small subset of proteins that possess a high degree of similarity [58-60].”

“[23] and others in the literature [23,51,52], we find that 5 of our 12 top compound-target predictions were validated (Supplementary Table 1 in Additional file 1).”

“This COX alteration has been shown to be linked to clozapine's side effects [66,67].”

“thought to be neurotransmitter receptors, but the drug also alters cytochome C oxidase (COX) activity through an unknown mechanism [65].”

“The fact that signal transduction is predicted relatively well by co-fitness, for example, may be explained by the fact that signal transduction is often a rapid response occurring on the order of milliseconds, a time frame too short to allow expression and translation of required proteins [53,54].”

“Combining our overexpression rescue results with those of Hoon et al. [23] and others in the literature [23, 51 ,52], we find that 5 of our 12 top compound-target predictions were validated (Supplementary Table 1 in Additional file 1). For the purposes of comparison, Hoon et al. [23] found overexpression resistance fo…”

“cerevisiae (16, 17) and hundreds have been performed in the bacteria Shewanella oneidensis MR-1 and Zymomonas mobilis ZM4 (1), far more than have been done with TnSeq approaches to date.”

“Last, a recent approach used information on compound-induced fitness defects of yeast deletion strains to predict drug-targets in S. cerevisiae (Hillenmeyer et al., 2010).”

“These approaches also unraveled stress response mechanisms and provided new insights into drug susceptibility and morphogenesis [42–49].”