Gene Expression and evolution of antifungal drug resistance
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE12055 | GEO | 2008/07/28
SECONDARY ACCESSION(S): PRJNA113385
REPOSITORIES: GEO
Similar Datasets
Project description:Liposomal amphotericin B is an important frontline drug for the treatment of visceral leishmaniasis, a neglected disease of poverty. The mechanism of action of amphotericin B (AmB) is thought to involve interaction with ergosterol and other ergostane sterols, resulting in disruption of the integrity and key functions of the plasma membrane. Emergence of clinically refractory isolates of L. donovani and L. infantum is an ongoing issue and knowledge of potential resistance mechanisms can help to alleviate this problem. Here we report the characterisation of four independently selected L. donovani clones that are resistant to AmB. Whole genome sequencing revealed that in three of the moderately resistant clones, resistance was due solely to the deletion of a gene encoding C24-sterol methyltransferase (SMT1). The fourth, hyper-resistant resistant clone (>60-fold) was found to have a 24 bp deletion in both alleles of a gene encoding a putative cytochrome P450 reductase (P450R1). Metabolic profiling indicated these parasites were virtually devoid of ergosterol (0.2% versus 18% of total sterols in wild-type) and had a marked accumulation of 14-methylfecosterol (75% versus 0.1% of total sterols in wild-type) and other 14-alpha methylcholestanes. These are substrates for sterol 14-alpha demethylase (CYP51) suggesting that this enzyme is a bona fide P450R specifically involved in electron transfer from NADPH to CYP51 during catalysis. Deletion of P450R1 in wild-type cells phenocopied the metabolic changes observed in our AmB hyper-resistant clone as well as in CYP51 nulls. Likewise, addition of a wild type P450R1 gene restored sterol profiles to wild type. Our studies indicate that P450R1 is essential for L. donovani amastigote viability, thus loss of this gene is unlikely to be a driver of clinical resistance. Nevertheless, investigating the mechanisms underpinning AmB resistance in these cells provided insights that refine our understanding of the L. donovani sterol biosynthetic pathway.
2024-06-21 | PXD052472 | Pride
Project description:Fluconazole (FLC), a triazole antifungal drug, is widely used for the maintenance therapy of cryptococcal meningoencephalitis, the most common opportunistic infection in AIDS patients, but this usage predisposes to the appearance of FLC resistance, especially in patients with no or limited access to highly active antiretroviral therapy. We used microarray analysis to examine changes in the gene expression profile of C. neoformans reference strain H99 (serotype A) following exposure to FLC in order to study the adaptive cellular responses to drug stress. Simultaneous analysis of over 6,823 C. neoformans gene transcript levels revealed that 476 genes were responsive to FLC. Up-regulated expression was observed, as expected, for genes involved in the ergosterol biosynthesis, including ERG13, ERG1, ERG7, ERG25, ERG2, ERG3, ERG5, and that encoding the azole target, ERG11, but also for the gene SRE1, that encodes a well-known regulator of sterol homeostasis in C. neoformans. In addition, several genes such as those involved in a wide variety of important cellular processes (i.e., lipid and fatty acid metabolism, cell wall maintenance, stress, virulence, etc.), were found to be up-regulated in response to fluconazole treatment. Some of these genes may represent potential therapeutic targets to be exploited in anticryptococcal therapy. Conversely, expression of AFR1, the major transporter of azoles in C. neoformans, was shown to be not affected by exposure to FLC, thus suggesting a minor involvement in the C. neoformans short-term adaptation to the azole drug. We studied the transient response of C. neoformans to fluconazole by analyzing differences in gene expression prior to and after exposure of strain H99. Three biological replicates were performed for each condition (FLC-exposed and -not exposed (controls)). The cells were exposed to 10 µg of FLC/ml (1/2 x MIC) or distilled water (controls) for one doubling time (90 min).
2010-11-15 | E-GEOD-24927 | biostudies-arrayexpress
Project description:Amphotericin B (AMB) is the most widely used polyene antifungal drug for the treatment of systemic fungal infections including invasive aspergillosis. We aimed to understand molecular targets of AMB in Aspergillus fumigatus (Afu) by genomic approaches. Amphotericin B (AMB) is the most widely used polyene antifungal drug for the treatment of systemic fungal infections including invasive aspergillosis. We aimed to understand molecular targets of AMB in Aspergillus fumigatus (Afu) by microarray and proteomic methods. Keywords: Aspergillus fumigatus treated with amphotericin B for 24 hours Experiment was performed in dye swap manner from two different biological replicates
2010-05-26 | E-GEOD-10505 | biostudies-arrayexpress
Project description:Fluconazole (FLC), a triazole antifungal drug, is widely used for the maintenance therapy of cryptococcal meningoencephalitis, the most common opportunistic infection in AIDS patients, but this usage predisposes to the appearance of FLC resistance, especially in patients with no or limited access to highly active antiretroviral therapy. We used microarray analysis to examine changes in the gene expression profile of C. neoformans reference strain H99 (serotype A) following exposure to FLC in order to study the adaptive cellular responses to drug stress. Simultaneous analysis of over 6,823 C. neoformans gene transcript levels revealed that 476 genes were responsive to FLC. Up-regulated expression was observed, as expected, for genes involved in the ergosterol biosynthesis, including ERG13, ERG1, ERG7, ERG25, ERG2, ERG3, ERG5, and that encoding the azole target, ERG11, but also for the gene SRE1, that encodes a well-known regulator of sterol homeostasis in C. neoformans. In addition, several genes such as those involved in a wide variety of important cellular processes (i.e., lipid and fatty acid metabolism, cell wall maintenance, stress, virulence, etc.), were found to be up-regulated in response to fluconazole treatment. Some of these genes may represent potential therapeutic targets to be exploited in anticryptococcal therapy. Conversely, expression of AFR1, the major transporter of azoles in C. neoformans, was shown to be not affected by exposure to FLC, thus suggesting a minor involvement in the C. neoformans short-term adaptation to the azole drug.
2010-11-15 | GSE24927 | GEO
Project description:Amphotericin B (AMB) is the most widely used polyene antifungal drug for the treatment of systemic fungal infections including invasive aspergillosis. We aimed to understand molecular targets of AMB in Aspergillus fumigatus (Afu) by genomic approaches. Keywords: Aspergillus fumigatus treated with amphotericin B for 24 hours
2008-02-14 | GSE10505 | GEO
Project description:Candida auris is an emerging multidrug-resistant human fungal pathogen often refractory to treatment by all classes of antifungal drugs. Amphotericin B (AmB) is a fungicidal drug that, despite its toxic side effects, remains a drug of choice for the treatment of drug-resistant fungal infections, including those caused by C. auris. However, the molecular mechanisms underlying AmB resistance are poorly understood. In this study, we present data that suggests membrane lipid alterations and chromatin modifications are critical processes that contribute to or cause adaptive AmB resistance in clinical C. auris isolates. To determine the plausible cause of increased AmB resistance, we performed RNA-seq of AmB-resistant and sensitive C. auris isolates. Remarkably, AmB-resistant strains show a pronounced enrichment of genes involved in lipid and ergosterol biosynthesis, adhesion, drug transport as well as chromatin remodeling. The transcriptomics data confirm increased adhesion and reduced lipid membrane permeability of AmB-resistant strains compared to the sensitive isolates. The AmB-resistant strains also display hyper-resistance to cell wall perturbing agents, including congo red, calcofluor white and caffeine. Additionally, we noticed an increased phosphorylation of Mkc1 cell integrity MAP kinase upon AmB treatment. Collectively, these data identify differences in the transcriptional landscapes of AmB-resistant vs AmB-senstive isolates, and provide a framework for the mechanistic understanding of AmB resistance in C. auris.
2022-05-02 | GSE190920 | GEO
Project description:<p>Amphotericin B is increasingly used in treatment of leishmaniasis. Here, fourteen independent lines of <em>Leishmania mexicana</em> and one <em>L. infantum</em> line were selected for resistance to either amphotericin B or the related polyene antimicrobial, nystatin. Sterol profiling revealed that, in each line, the predominant ergostane-type sterol of wild-type cells was replaced by other sterol species. Broadly, two different profiles emerged among the resistant lines. Whole genome sequencing then showed that these distinct profiles were due either to mutations in the sterol methyl transferase (C24SMT) gene locus or the sterol C5 desaturase (C5DS) gene. In three lines an additional deletion of the miltefosine transporter was found. Differences in sensitivity to amphotericin B were apparent, depending on whether cells were grown in HOMEM, supplemented with foetal bovine serum, or a serum free defined medium (DM). These differences appeared to relate to the presence of lipids in the former. Metabolomic analysis after exposure to AmB showed that a large increase in glucose flux via the pentose phosphate pathway preceded cell death in cells sustained in HOMEM but not DM, indicating the oxidative stress was more significantly induced under HOMEM conditions. Several of the lines were tested for ability to infect macrophages and replicate as amastigote forms, alongside their ability to establish infections in mice. While several lines showed reduced virulence, at least one AmB resistant line displayed heightened virulence in mice whilst retaining its resistance phenotype, emphasising the risks of resistance emerging to this critical drug.</p>
2022-09-22 | MTBLS2744 | MetaboLights
Project description:<p><strong>BACKGROUND:</strong> Protozoan Leishmania parasites are responsible for a range of clinical infections that represent a substantial challenge for global health. Amphotericin B (AmB) is increasingly used to treat Leishmania infection, so understanding the potential for resistance to this drug is an important priority. Previously we described four independently-derived AmB-resistant L. mexicana lines that exhibited resistance-associated genetic lesions resulting in altered sterol content. However, substantial phenotypic variation between these lines, including differences in virulence attributes, were not fully explained by these changes.</p><p><strong>METHODS:</strong> To identify alterations in cellular metabolism potentially related to phenotypic differences between wild-type and AmB-resistant lines, we extracted metabolites and performed untargeted metabolomics by liquid chromatography-mass spectrometry.</p><p><strong>RESULTS:</strong> We observed substantial differences in metabolite abundance between lines, arising in an apparently stochastic manner. Concerted remodeling of central carbon metabolism was not observed; however, in three lines, decreased abundance of several oligohexoses was observed. Given that the oligomannose mannogen is an important virulence factor in Leishmania, this could relate to loss of virulence in these lines. Increased abundance of the reduced forms of the oxidative stress-protective thiols trypanothione and glutathione was also observed in multiple lines.</p><p><strong>CONCLUSIONS:</strong> This dataset will provide a useful resource for understanding the molecular basis of drug resistance in Leishmania, and suggests a role for metabolic changes separate from the primary mechanism of drug resistance in determining the phenotypic profile of parasite lines subjected to experimental selection of resistance.</p>
2019-09-26 | MTBLS1167 | MetaboLights
Project description:Invasive fungal infections (IFIs) are difficult to treat. Few effective antifungal drugs are available and many have problems with toxicity, efficacy and drug-resistance. To overcome these challenges, existing therapies may be enhanced using more than one agent acting in synergy. Previously, we have found amphotericin B (AMB) and the iron chelator, lactoferrin (LF), were synergistic against Cryptococcus neoformans and Saccharomyces cerevisiae. This study investigates the mechanism of AMB+LF synergy using RNA-seq in Cryptococcus neoformans H99.
2019-09-08 | GSE130375 | GEO
Project description:Cryptococcus neoformans (Cn) is an opportunistic fungal microorganism that causes life-threatening meningoencephalitis. During the infection, the microbial population is heterogeneously composed of cells with varying generational ages, with older cells accumulating during chronic infections. This is attributed to their enhanced resistance to phagocytic killing and tolerance of antifungals like fluconazole (FLC). Using RNA-seq, we investigated how transcriptomic changes in different aspects of metabolism contribute to age-associated FLC tolerance in Cn.
2024-03-06 | GSE260902 | GEO