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Project description:Abstract: Chemogenomic fitness assays were combined with a transcriptome analysis to understand both the mode of action and the mechanisms of resistance to Chitosan oligosaccharides (COS). COS are deacetylated chitin compounds, with antimicrobial properties, that are presumed to act by disrupting the cell membrane. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified encode membrane proteins and members of the protein degradation/ proteosome pathway. The transcriptomes of wild-type and five suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and furthermore, treatment with environmental stressors does not provide resistance to COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the RAS signal transduction pathway. Down-regulated transcripts included those encoding protein folding components, and respiratory chain proteins. Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to amphotericin B, fluconazole and terbinafine as the wild-type (vector control). The gene targets of COS identified in this study suggest that COSM-bM-^@M-^Ys mechanism of action is different from other commonly studied fungicides, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens. We selected the 5 overexpressing strains based on the characteristics of the genes. ARL1, encoding a GTPase and is involved in membrane trafficking, was selected since it was observed in the HIP-HOP assay as a sensitive homozygous deletion strain and in the MSP assay as multicopy suppressor. The rest of selected overexpressing strains were BCK2 and MSG5, involved in cell integrity pathways, ERG24 in ergosterol synthesis, and RBA50 in transcription. BCK2 is a Ser-Thr rich protein with protein kinase C activity that acts in signal transduction. Overexpression of BCK2 can rescue defects in yeast cwh43M-NM-^T, which displays several cell wall defects [29]. BCK2 overexpression also can suppress a cell lysis defect of mpk1M-NM-^T and pck1M-NM-^T [30]. MSG5 is also involved in signal transduction. This gene encodes a protein phosphatase involved in cell cycle control through the dephosphorylation of MAPK and is indispensable for restricting the signaling by the cell integrity pathway in yeast [31]. The inhibition of MAPK signaling leads to inhibition of cell differentiation and cell division [32]. The functions of ARL1 and ERG24 and their potential roles in chitosan resistance will be described in more detail in the Discussion. To gain a further understanding on the mode of action and mechanisms of resistance to COS, we performed a transcriptome analysis of the above mentioned five overexpressing strains known to increase resistance to COS-5.44. Each overexpressing strain and the wild type (vector control) were treated with COS-5.44 and RNAs isolated from both treated and untreated cells. The RNAs were converted to labeled cDNA and hybridized to NimbleGen expression microarrays (see Methods). Three cDNA biological replicates either with or without a 60 minutes exposure to COS-5.44 for each of the five overexpressing strains as well as an untransformed wild type BY4743 cells (vector control; for a total of 36 samples) were hybridized to NimbleGen 4X72k microarrays (Roche NimbleGen, Inc. Design ID A6186-00-01, TI4932 60mer expr X4).
2012-12-22 | E-GEOD-32888 | biostudies-arrayexpress
Project description:Abstract: Chemogenomic fitness assays were combined with a transcriptome analysis to understand both the mode of action and the mechanisms of resistance to Chitosan oligosaccharides (COS). COS are deacetylated chitin compounds, with antimicrobial properties, that are presumed to act by disrupting the cell membrane. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified encode membrane proteins and members of the protein degradation/ proteosome pathway. The transcriptomes of wild-type and five suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and furthermore, treatment with environmental stressors does not provide resistance to COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the RAS signal transduction pathway. Down-regulated transcripts included those encoding protein folding components, and respiratory chain proteins. Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to amphotericin B, fluconazole and terbinafine as the wild-type (vector control). The gene targets of COS identified in this study suggest that COS’s mechanism of action is different from other commonly studied fungicides, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens. We selected the 5 overexpressing strains based on the characteristics of the genes. ARL1, encoding a GTPase and is involved in membrane trafficking, was selected since it was observed in the HIP-HOP assay as a sensitive homozygous deletion strain and in the MSP assay as multicopy suppressor. The rest of selected overexpressing strains were BCK2 and MSG5, involved in cell integrity pathways, ERG24 in ergosterol synthesis, and RBA50 in transcription. BCK2 is a Ser-Thr rich protein with protein kinase C activity that acts in signal transduction. Overexpression of BCK2 can rescue defects in yeast cwh43Δ, which displays several cell wall defects [29]. BCK2 overexpression also can suppress a cell lysis defect of mpk1Δ and pck1Δ [30]. MSG5 is also involved in signal transduction. This gene encodes a protein phosphatase involved in cell cycle control through the dephosphorylation of MAPK and is indispensable for restricting the signaling by the cell integrity pathway in yeast [31]. The inhibition of MAPK signaling leads to inhibition of cell differentiation and cell division [32]. The functions of ARL1 and ERG24 and their potential roles in chitosan resistance will be described in more detail in the Discussion. To gain a further understanding on the mode of action and mechanisms of resistance to COS, we performed a transcriptome analysis of the above mentioned five overexpressing strains known to increase resistance to COS-5.44. Each overexpressing strain and the wild type (vector control) were treated with COS-5.44 and RNAs isolated from both treated and untreated cells. The RNAs were converted to labeled cDNA and hybridized to NimbleGen expression microarrays (see Methods).
2012-12-22 | GSE32888 | GEO
Project description:Anaplastic lymphoma kinase (ALK) inhibitors (ALKi) are effective in treating lung cancer patients with chromosomal rearrangement of ALK. However, continuous treatment with ALKi invariably leads to acquired resistance in cancer cells. In this study, we propose an efficient strategy to suppress ALKi resistance through a meta-analysis of transcriptome data from various cell models of acquired resistance to ALKi. We systematically identified gene signatures that consistently showed altered expression during the development of resistance and conducted computational drug screening using these signatures. We identified emetine as a promising candidate compound to inhibit the growth of ALKi-resistant cells. We demonstrated that this drug exhibited effectiveness in inhibiting the growth of ALKi-resistant cells, and further elucidated its mode of action through drug-induced RNA-seq data. Our transcriptome-guided systematic approach paves the way for efficient drug discovery to overcome acquired resistance to cancer therapy.
2024-01-09 | GSE252540 | GEO
Project description:This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/The drug Praziquantel is the most commonly used drug for parasitic flatworms. It is currently being increasingly used in mass drug administration programmes, raising concerns over whether resistance will develop. Although widely used, its mode of action was until very recently uncertain. This study will investigate the praziquantel mode of action and resistance by sequencing the transcriptomes of Dugesia japonica and different stages and strains of S. mansoni.
2013-05-13 | E-ERAD-135 | biostudies-arrayexpress
Project description:Praziquantel mode of action and resistance
| PRJEB1281 | ENA
Project description:The global prevalence of antibacterial resistance requires new antibacterial drugs with novel chemical scaffolds and modes of action. It is also vital to design compounds with optimal physicochemical properties to permeate the bacterial cell envelope. We described an approach of combining and integrating whole cell screening and metabolomics into early antibacterial drug discovery using a library of small polar compounds. Whole cell screening of a diverse library of small polar compounds against <i>Staphylococcus aureus</i> gave compound <b>2</b>. Hit expansion was carried out to determine structure-activity relationships. A selection of compounds from this series, together with other screened active compounds, was subjected to an initial metabolomics study to provide a metabolic fingerprint of the mode of action. It was found that compound <b>2</b> and its analogues have a different mode of action from some of the known antibacterial compounds tested. This early study highlighted the potential of whole cell screening and metabolomics in early antibacterial drug discovery. Future works will require improving potency and performing orthogonal studies to confirm the modes of action.
2021-11-04 | MTBLS788 | MetaboLights
Project description:Deciphering the mode of action (MOA) of new antibiotics discovered through phenotypic screening is of increasing importance. Metabolomics offers a potentially rapid and cost-effective means of identifying modes of action of drugs whose effects are mediated through changes in metabolism. Metabolomics techniques also collect data on off-target effects and drug modifications. Here, we present data from an untargeted liquid chromatography-mass spectrometry approach to identify the modes of action of eight compounds: 1-[3-fluoro-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)phenyl]-3-[2-(trifluoromethyl)phenyl]urea (AZ1), 2-(cyclobutylmethoxy)-5'-deoxyadenosine, triclosan, fosmidomycin, CHIR-090, carbonyl cyanidem-chlorophenylhydrazone (CCCP), 5-chloro-2-(methylsulfonyl)-N-(1,3-thiazol-2-yl)-4-pyrimidinecarboxamide (AZ7), and ceftazidime. Data analysts were blind to the compound identities but managed to identify the target as thymidylate kinase for AZ1, isoprenoid biosynthesis for fosmidomycin, acyl-transferase for CHIR-090, and DNA metabolism for 2-(cyclobutylmethoxy)-5'-deoxyadenosine. Changes to cell wall metabolites were seen in ceftazidime treatments, although other changes, presumably relating to off-target effects, dominated spectral outputs in the untargeted approach. Drugs which do not work through metabolic pathways, such as the proton carrier CCCP, have no discernible impact on the metabolome. The untargeted metabolomics approach also revealed modifications to two compounds, namely, fosmidomycin and AZ7. An untreated control was also analyzed, and changes to the metabolome were seen over 4 h, highlighting the necessity for careful controls in these types of studies. Metabolomics is a useful tool in the analysis of drug modes of action and can complement other technologies already in use.
2017-06-16 | MTBLS464 | MetaboLights
Project description:A systematic approach allowing the identification of the molecular way of action of novel potential drugs still represents the golden-tool for drug-discovery researchers. While high-throughput screening technologies of large libraries is now well established, the assessment of the drug targets and mechanism of action is still under development. Taking advantage of the yeast model Saccharomyces cerevisiae, we herein applied BarSeq, a Next Generation Sequencing based method to the analysis of both haploinsufficiency and homozygous fitness effects of a novel antifungal drug compared to the well-known antifungal, ketoconazole. Integrative bioinformatic analysis of BarSeq, whole genome expression analysis and classical biological assays identified the target and cell pathways affected by the novel antifungal. Confirmation of the effects observed in the yeast model as well as in pathogenic fungi further demonstrated the reliability of the multi-sided approach and the novelty of the targets and mode of action of the new class of molecules studied that thus represent a valuable source of novel antifungals.
2016-12-30 | GSE42418 | GEO
Project description:Here we report an approach that has permitted us to uncover the sites and mechanisms of action of a drug, referred to as SD70, initially identified by phenotypic screening for inhibitors of ligand and genotoxic stress-induced translocations in prostate cancer cells. Based on synthesis of a derivatized form of SD70 that permits its application for a ChIP-seq-like approach, referred to as Drug-seq, we were next able to efficiently map the genome-wide binding locations of this small molecule, revealing that it largely co-localized with androgen receptor (AR) on regulatory enhancers. Based on these observations, we performed the appropriate global analyses to ascertain that SD70 inhibits the androgen-dependent AR program, and prostate cancer cell growth, acting, at least in part, by functionally inhibiting the jumonji (JMJ) domain-containing demethylase, KDM4C. Drug-seq represents a powerful strategy for new drug development by mapping genome-wide location of small molecules, a powerful adjunct to contemporary drug development strategies. Drug-seq assay followed by high-throughput sequencing (HT-seq).
2014-07-01 | E-GEOD-55901 | biostudies-arrayexpress
Project description:We combined a mechanism-based and a cell-based drug screening coupled to a computational analysis, which allowed to identify potential drugs and metabolic pathways relevant for the pathophysiology of nephropathic cystinosis. This result was achieved by comparing gene-expression signature of lead compounds that share common mechanisms of action or that involve similar pathways with the disease gene-expression signature revealed by RNA-seq.
2021-11-26 | GSE184805 | GEO