Comparative transcriptional analysis of Candida auris biofilms following farnesol and tyrosol treatment
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ABSTRACT:
PROVIDER: PRJNA976246 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24739172.fastq.gz | Fastqsanger.gz | |||
| SRR24739173.fastq.gz | Fastqsanger.gz | |||
| SRR24739174.fastq.gz | Fastqsanger.gz | |||
| SRR24739175.fastq.gz | Fastqsanger.gz | |||
| SRR24739176.fastq.gz | Fastqsanger.gz |
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Project description:Candida auris is frequently associated with biofilm-related invasive infections. The resistant profile of these biofilms necessitates innovative therapeutic options, where quorum sensing may be a potential target. Farnesol and tyrosol are two fungal quorum-sensing molecules with antifungal effects at supraphysiological concentrations. Here, we performed genome-wide transcript profiling with C. auris biofilms following farnesol or tyrosol exposure using transcriptome sequencing (RNA-Seq). Since transition metals play a central role in fungal virulence and biofilm formation, levels of intracellular calcium, magnesium, and iron were determined following farnesol or tyrosol treatment using inductively coupled plasma optical emission spectrometry. Farnesol caused an 89.9% and 73.8% significant reduction in the calcium and magnesium content, respectively, whereas tyrosol resulted in 82.6%, 76.6%, and 81.2% decrease in the calcium, magnesium, and iron content, respectively, compared to the control. Genes involved in biofilm events, glycolysis, ergosterol biosynthesis, fatty acid oxidation, iron metabolism, and autophagy were primarily affected in treated cells. To prove ergosterol quorum-sensing molecule interactions, microdilution-based susceptibility testing was performed, where the complexation of farnesol, but not tyrosol, with ergosterol was impeded in the presence of exogenous ergosterol, resulting in a minimum inhibitory concentration increase in the quorum-sensing molecules. This study revealed several farnesol- and tyrosol-specific responses, which will contribute to the development of alternative therapies against C. auris biofilms.
2023-12-11 | GSE233427 | GEO
Project description:The antifungal resistance threat posed by Candida auris necessitates bold and innovative therapeutic options. Farnesol, a quorum-sensing molecule with a potential antifungal and/or adjuvant effect; it may be a promising candidate in alternative treatment regimens. To gain further insights into the farnesol-related effect on C. auris, genome-wide gene expression analysis was performed using RNA-Seq. Farnesol exposure resulted in 1,766 differentially expressed genes. Of these, 447 and 304 genes with at least 1.5-fold increase or decrease in expression, respectively, were selected for further investigation. Genes involved in morphogenesis, biofilm events (maturation and dispersion), gluconeogenesis, iron metabolism, and regulation of RNA biosynthesis showed down-regulation, whereas those related to antioxidative defense, transmembrane transport, glyoxylate cycle, fatty acid β-oxidation, and peroxisome processes were up-regulated. In addition, farnesol treatment increased the expression of certain efflux pump genes, including MDR1, CDR1, and CDR2. Growth, measured by change in CFU number, was significantly inhibited within 2 hours of the addition of farnesol (5.8×10^7±1.1×10^7 and 1.1×10^7±0.3×10^7 CFU/ml for untreated control and farnesol-exposed cells, respectively) (p<0.001). In addition, farnesol treatment caused a significant reduction in intracellular iron (152.2±21.1 vs. 116.0±10.0 mg/kg), manganese (67.9±5.1 vs. 18.6±1.8 mg/kg), and zinc (787.8±22.2 vs. 245.8±34.4 mg/kg) (p<0.05–0.001) compared to untreated control cells, whereas the level of cooper was significantly increased (274.6±15.7 vs. 828.8±106.4 mg/kg) (p<0.001). Our data demonstrate that farnesol significantly influences the growth, intracellular metal ion contents, and gene expression related to fatty acid metabolism, which could open new directions in developing alternative therapies against C. auris.
2021-09-30 | GSE180093 | GEO
Project description:Tyrosol, a secondary metabolite of Candida species, regulates fungal morphogenesis, and its application may represent a novel innovative therapy against emerging multi-resistant fungal superbug such as Candida auris. In the current study, the effects of tyrosol on growth, redox homeostasis, intracellular microelement contents and activities of virulence-related enzymes released by C. auris were examined. To gain further information about the effect of tyrosol exposure, we revealed gene transcriptional changes using total transcriptome sequencing (RNA-Seq). At a concentration of 15 mM, tyrosol significantly decrease the growth of fungal cells within 2 h of its addition (5.6 × 107±1.2 × 107 and 2.5 × 107±0.6 × 107 colony forming unit/mL for control and tyrosol-treated cells, respectively). Furthermore, it enhanced the release of reactive oxygen species as confirmed by a dichlorofluorescein (DCF) assay (7.3 ± 1.8 [nmol DCF (OD640)−1] versus 16.8 ± 3.9 [nmol DCF (OD640)−1]), which was coincided with elevated superoxide dismutase, catalase and glutathione peroxidase activities. Tyrosol exerted in a 37%, 25%, 34% and 55% decrease in intracellular manganese, iron, zinc and copper contents, respectively, compared to control cells. The tyrosol treatment led to a 142 and 108 differentially transcripted genes with at least a 1.5-fold increase or decrease in transcription, respectively. Genes related to iron and fatty acid metabolism as well as nucleic acid synthesis were down-regulated, whereas those related to the antioxidative defence, adhesion and oxoacid metabolic processes were up-regulated. This study shows that tyrosol significantly influences growth, intracellular physiological processes and gene transcription in C. auris, which could highly support the development of novel treatment approaches against this important pathogen.
2023-07-31 | GSE223953 | GEO
Project description:In this study, we designed a novel antifungal agent, PQA-Az-13 that demonstrated antifungal activity against C. auris biofilms. Cellular proteomics indicated that PQA-Az-13 partially or completely inhibited numerous enzymatic proteins in C. auris biofilms, particularly those involved in both amino acid biosynthesis and metabolism processes, as well as in general energy-producing processes. Due to its hydrophobic nature and limited aqueous solubility, PQA-Az-13 was encapsulated in cationic liposomes and characterized by biophysical and spectral techniques. PQA-Az-13 liposomes demonstrated enhanced antifungal activity levels against both C. auris in in vitro biofilms and ex vivo skin colonization models.
2023-12-07 | PXD046911 | Pride
Project description:The World Health Organization (WHO) had designated Candida auris as a critical public health threat due to its multidrug resistance to antifungal agents, high mortality rate, and its ability to cause nosocomial outbreaks. A matter of serious concern is that conventional antifungal monotherapies is frequently ineffective against biofilm-associated C. auris infection, highlighting the need for more effective strategies. Combination therapies have demonstrated improved efficacy and specificity, and may also slow the development of antifungal resistance. Therefore, this study aimed to evaluate the in vitro and in vivo efficacy of caspofungin (CAS) and posaconazole (POSA) in combination against sessile C. auris isolates from the South Asian clade and to characterize the associated transcriptomic responses. The CAS with POSA combination resulted in a significant reduction in median minimum inhibitory concentrations (4–32-fold for CAS and 8–64-fold for POSA) compared to monotherapies. Synergistic interactions were observed in all isolates tested, with fractional inhibitory concentration indices ranging from 0.078 to 0.31. In line with the in vitro findings, synergistic interactions were confirmed by in vivo experiments. The fungal kidney burden decreases were three log volumes in mice treated with combination of 1 mg/kg/day caspofungin and 1.5 mg/kg/day posaconazole. To investigate the gene expression changes in response to combination treatment, 612 genes showed increased expression and 465 genes were downregulated relative to the untreated control biofilms (fold change >1.5 or <–1.5). Notably, genes involved in biofilm dispersion, oxidative stress response, iron metabolism, and glycolysis were downregulated, whereas those associated with cell wall organization or biogenesis, osmotic stress response, calcium signaling, drug efflux, biofilm formation, and the biosynthesis of ergosterol and chitin were upregulated. These findings demonstrate the potent synergistic activity of CAS and POSA against C. auris biofilms and provide insight into C. auris antifungal therapeutic responses, thereby contributing to the development of more effective antifungal treatment strategies.
2025-09-01 | GSE302377 | GEO
Project description:We used the results of a genome sequence survey to design and manufacture partial genomic microarrays that were applied to determining the transcriptional response of C. parapsilosis to the presence of exogenous farnesol. Keywords: drug response, farnesol,
2007-03-01 | GSE6318 | GEO
Project description:Transcriptional profiling of the Candida auris response to exogenous farnesol exposure
| PRJNA746543 | ENA
Project description:We used the results of a genome sequence survey to design and manufacture partial genomic microarrays that were applied to determining the transcriptional response of C. parapsilosis to the presence of exogenous farnesol. Keywords: drug response, farnesol, Transcriptional profiling was performed following exposure to 50 microM of farnesol compare to the control experiment (no treatment). Six independent experiment comparisons (including 3 dye swaps) were performed.
2010-06-11 | E-GEOD-6318 | biostudies-arrayexpress
Project description:Candida auris is an enigmatic fungal pathogen, recently elevated to the Critical Priority group of fungal pathogens by the World Health Organisation. Of key concern is its ability to cause outbreaks within intensive and chronic care units, which is facilitated through biofilm formation. We investigated the susceptibility of phenotypically-diverse C. auris isolates to sodium hypochlorite (NaOCl) disinfection, and the subsequent role of biofilms in surviving disinfection using a dry-surface biofilm (DSB) model and transcriptomic profiling. Planktonic cells were tested for susceptibility to NaOCl using minimum inhibitory concentration and disinfection protocols. Biofilm formation using the DSB model consisted of consecutive 48 hr cycles with/without media across a 12-day period, assessed using viable counts, biomass assays, and microscopy. Disinfection efficacy was assessed using clinically relevant protocols of 500-1000 ppm for 1-5 min. RNA-sequencing was performed on untreated DSBs in comparison to planktonic cells. Isolates were found to be sensitive to NaOCl planktonically at concentrations ≤62.5 ppm, and grew robust biofilms using the DSB protocol. Biofilms developed tolerance to all NaOCl treatment parameters, with 2-4 log10-reductions in viable cells observed at highest concentrations. Transcriptomics identified ABC transporters and iron acquisition pathways as strongly upregulated in DSBs relative to planktonic cells. We have optimised a DSB protocol in which C. auris biofilms can mediate tolerance to adverse conditions such as NaOCl disinfection, suggesting a lifestyle through which this problematic yeast can environmentally persist and transmit. Mechanistically, the upregulation of small-molecule and iron transport pathways have been identified as potential facilitators of survival.
2023-08-07 | GSE239851 | GEO
Project description:Candida auris occupies similar niches in various infections as Pseudomonas aeruginosa; however, the details of their interspecies communication remain largely unknown. To gain deeper insights into this bacterial–fungal relationship, phenotypic and transcriptomic analyses were conducted in the presence of the primary P. aeruginosa quorum-sensing molecule, 3-oxo-C12-homoserine lactone (HSL), against C. auris, with the results compared to those of C. albicans. We demonstrated a significant HSL-induced reduction in adhesion of C. auris cells at 100- and 200-μM concentrations. Furthermore, HSL exposure reduced intracellular iron and zinc levels and modulated C. auris metabolism toward beta-oxidation, which may be associated with the observed reduction in in vivo virulence at lower HSL concentrations compared with C. albicans. RNA-sequencing transcriptome analysis revealed 67 and 306 upregulated genes, as well as 111 and 168 downregulated genes, in response to 100 and 200 μM HSL, respectively. We identified 45 overlapping upregulated and 25 overlapping downregulated genes between the two HSL concentrations. Our findings indicate that HSL-induced effects are not specific to C. albicans; additionally, several characteristics are present in C. auris but not in C. albicans following HSL exposure. Similar to other Candida-derived C12 compounds (e.g., farnesol), HSL reduces several C. auris survival strategies, which may significantly influence the nature of P. aeruginosa–C. auris co-habitation.
2024-07-10 | GSE271513 | GEO