Sample File "FungiNet_template_RNA-seq_V1.9_Ex_ID_005"

Cultivation of A. fumigatus in an O2-controlled fermenter and analysed its minute-scale responses to O2 limitation. Transcriptome sequencing revealed a group of genes underlying a rapid and highly dynamic regulation.

Creators: Jörg Linde, Falk Hillmann, Olaf Kniemeyer

Submitter: Maja Rey

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From environmental adaptation to host survival: Attributes that mediate pathogenicity of Candida auris.

Abstract (Expand)

Candida species are a major cause of invasive fungal infections. While Candida albicans, C. glabrata, C. parapsilosis, and C. tropicalis are the most dominant species causing life-threatening candidiasis, … C. auris recently emerged as a new species causing invasive infections with high rates of clinical treatment failures. To mimic initial phases of systemic Candida infections with dissemination via the bloodstream and to elucidate the pathogenic potential of C. auris, we used an ex vivo whole blood infection model. Similar to other clinically relevant Candida spp., C. auris is efficiently killed in human blood, but showed characteristic patterns of immune cell association, survival rates, and cytokine induction. Dual-species transcriptional profiling of C. auris-infected blood revealed a unique C. auris gene expression program during infection, while the host response proofed similar and conserved compared to other Candida species. C. auris-specific responses included adaptation and survival strategies, such as counteracting oxidative burst of immune cells, but also expression of potential virulence factors, (drug) transporters, and cell surface-associated genes. Despite comparable pathogenicity to other Candida species in our model, C. auris-specific transcriptional adaptations as well as its increased stress resistance and long-term environmental survival, likely contribute to the high risk of contamination and distribution in a nosocomial setting. Moreover, infections of neutrophils with pre-starved C. auris cells suggest that environmental preconditioning can have modulatory effects on the early host interaction. In summary, we present novel insights into C. auris pathogenicity, revealing adaptations to human blood and environmental niches distinctive from other Candida species.

Authors: S. Allert, D. Schulz, P. Kammer, P. Grossmann, T. Wolf, S. Schauble, G. Panagiotou, S. Brunke, B. Hube

Date Published: 10th Feb 2022

Publication Type: Journal

Disruption of the Aspergillus fumigatus RNA interference machinery alters the conidial transcriptome.

Abstract (Expand)

The RNA interference (RNAi) pathway has evolved numerous functionalities in eukaryotes, with many on display in Kingdom Fungi. RNAi can regulate gene expression, facilitate drug resistance, or even be … altogether lost to improve growth potential in some fungal pathogens. In the WHO fungal priority pathogen, Aspergillus fumigatus, the RNAi system is known to be intact and functional. To extend our limited understanding of A. fumigatus RNAi, we first investigated the genetic variation in RNAi-associated genes in a collection of 217 environmental and 83 clinical genomes, where we found that RNAi components are conserved even in clinical strains. Using endogenously expressed inverted-repeat transgenes complementary to a conditionally essential gene (pabA) or a nonessential gene (pksP), we determined that a subset of the RNAi componentry is active in inverted-repeat transgene silencing in conidia and mycelium. Analysis of mRNA-seq data from RNAi double-knockout strains linked the A. fumigatus dicer-like enzymes (DclA/B) and RNA-dependent RNA polymerases (RrpA/B) to regulation of conidial ribosome biogenesis genes; however, surprisingly few endogenous small RNAs were identified in conidia that could explain this broad change. Although RNAi was not clearly linked to growth or stress response defects in the RNAi knockouts, serial passaging of RNAi knockout strains for six generations resulted in lineages with diminished spore production over time, indicating that loss of RNAi can exert a fitness cost on the fungus. Cumulatively, A. fumigatus RNAi appears to play an active role in defense against double-stranded RNA species alongside a previously unappreciated housekeeping function in regulation of conidial ribosomal biogenesis genes.

Authors: A. A. Kelani, A. Bruch, F. Rivieccio, C. Visser, T. Kruger, D. Weaver, X. Pan, S. Schauble, G. Panagiotou, O. Kniemeyer, M. J. Bromley, P. Bowyer, A. E. Barber, A. A. Brakhage, M. G. Blango

Date Published: 19th Jun 2023

Publication Type: Journal

Distinct transcriptional responses to fludioxonil in Aspergillus fumigatus and its DeltatcsC and Deltaskn7 mutants reveal a crucial role for Skn7 in the cell wall reorganizations triggered by this antifungal.

Abstract (Expand)

BACKGROUND: Aspergillus fumigatus is a major fungal pathogen that causes severe problems due to its increasing resistance to many therapeutic agents. Fludioxonil is a compound that triggers a lethal … activation of the fungal-specific High Osmolarity Glycerol pathway. Its pronounced antifungal activity against A. fumigatus and other pathogenic molds renders this agent an attractive lead substance for the development of new therapeutics. The group III hydride histidine kinase TcsC and its downstream target Skn7 are key elements of the multistep phosphorelay that represents the initial section of the High Osmolarity Glycerol pathway. Loss of tcsC results in resistance to fludioxonil, whereas a Deltaskn7 mutant is partially, but not completely resistant. RESULTS: In this study, we compared the fludioxonil-induced transcriptional responses in the DeltatcsC and Deltaskn7 mutant and their parental A. fumigatus strain. The number of differentially expressed genes correlates well with the susceptibility level of the individual strains. The wild type and, to a lesser extend also the Deltaskn7 mutant, showed a multi-faceted stress response involving genes linked to ribosomal and peroxisomal function, iron homeostasis and oxidative stress. A marked difference between the sensitive wild type and the largely resistant Deltaskn7 mutant was evident for many cell wall-related genes and in particular those involved in the biosynthesis of chitin. Biochemical data corroborate this differential gene expression that does not occur in response to hyperosmotic stress. CONCLUSIONS: Our data reveal that fludioxonil induces a strong and TcsC-dependent stress that affects many aspects of the cellular machinery. The data also demonstrate a link between Skn7 and the cell wall reorganizations that foster the characteristic ballooning and the subsequent lysis of fludioxonil-treated cells.

Authors: S. Schruefer, A. Pschibul, S. S. W. Wong, T. Sae-Ong, T. Wolf, S. Schauble, G. Panagiotou, A. A. Brakhage, V. Aimanianda, O. Kniemeyer, F. Ebel

Date Published: 14th Nov 2023

Publication Type: Journal

Pathogen-specific innate immune response patterns are distinctly affected by genetic diversity.

Abstract (Expand)

Innate immune responses vary by pathogen and host genetics. We analyze quantitative trait loci (eQTLs) and transcriptomes of monocytes from 215 individuals stimulated by fungal, Gram-negative or … Gram-positive bacterial pathogens. We identify conserved monocyte responses to bacterial pathogens and a distinct antifungal response. These include 745 response eQTLs (reQTLs) and corresponding genes with pathogen-specific effects, which we find first in samples of male donors and subsequently confirm for selected reQTLs in females. reQTLs affect predominantly upregulated genes that regulate immune response via e.g., NOD-like, C-type lectin, Toll-like and complement receptor-signaling pathways. Hence, reQTLs provide a functional explanation for individual differences in innate response patterns. Our identified reQTLs are also associated with cancer, autoimmunity, inflammatory and infectious diseases as shown by external genome-wide association studies. Thus, reQTLs help to explain interindividual variation in immune response to infection and provide candidate genes for variants associated with a range of diseases.

Authors: A. Hader, S. Schauble, J. Gehlen, N. Thielemann, B. C. Buerfent, V. Schuller, T. Hess, T. Wolf, J. Schroder, M. Weber, K. Hunniger, J. Loffler, S. Vylkova, G. Panagiotou, J. Schumacher, O. Kurzai

Date Published: 5th Jun 2023

Publication Type: Journal

Serum FHR1 binding to necrotic-type cells activates monocytic inflammasome and marks necrotic sites in vasculopathies.

Abstract (Expand)

Persistent inflammation is a hallmark of many human diseases, including anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV) and atherosclerosis. Here, we describe a dominant trigger of … inflammation: human serum factor H-related protein FHR1. In vitro, this protein selectively binds to necrotic cells via its N-terminus; in addition, it binds near necrotic glomerular sites of AAV patients and necrotic areas in atherosclerotic plaques. FHR1, but not factor H, FHR2 or FHR3 strongly induces inflammasome NLRP3 in blood-derived human monocytes, which subsequently secrete IL-1beta, TNFalpha, IL-18 and IL-6. FHR1 triggers the phospholipase C-pathway via the G-protein coupled receptor EMR2 independent of complement. Moreover, FHR1 concentrations of AAV patients negatively correlate with glomerular filtration rates and associate with the levels of inflammation and progressive disease. These data highlight an unexpected role for FHR1 during sterile inflammation, may explain why FHR1-deficiency protects against certain diseases, and identifies potential targets for treatment of auto-inflammatory diseases.

Authors: S. Irmscher, S. R. Brix, S. L. H. Zipfel, L. D. Halder, S. Mutluturk, S. Wulf, E. Girdauskas, H. Reichenspurner, R. A. K. Stahl, B. Jungnickel, T. Wiech, P. F. Zipfel, C. Skerka

Date Published: 4th Jul 2019

Publication Type: Not specified

Immune modulation by complement receptor 3-dependent human monocyte TGF-beta1-transporting vesicles.

Abstract (Expand)

Extracellular vesicles have an important function in cellular communication. Here, we show that human and mouse monocytes release TGF-beta1-transporting vesicles in response to the pathogenic fungus … Candida albicans. Soluble beta-glucan from C. albicans binds to complement receptor 3 (CR3, also known as CD11b/CD18) on monocytes and induces the release of TGF-beta1-transporting vesicles. CR3-dependence is demonstrated using CR3-deficient (CD11b knockout) monocytes generated by CRISPR-CAS9 genome editing and isolated from CR3-deficient (CD11b knockout) mice. These vesicles reduce the pro-inflammatory response in human M1-macrophages as well as in whole blood. Binding of the vesicle-transported TGF-beta1 to the TGF-beta receptor inhibits IL1B transcription via the SMAD7 pathway in whole blood and induces TGFB1 transcription in endothelial cells, which is resolved upon TGF-beta1 inhibition. Notably, human complement-opsonized apoptotic bodies induce production of similar TGF-beta1-transporting vesicles in monocytes, suggesting that the early immune response might be suppressed through this CR3-dependent anti-inflammatory vesicle pathway.

Authors: L. D. Halder, E. A. H. Jo, M. Z. Hasan, M. Ferreira-Gomes, T. Kruger, M. Westermann, D. I. Palme, G. Rambach, N. Beyersdorf, C. Speth, I. D. Jacobsen, O. Kniemeyer, B. Jungnickel, P. F. Zipfel, C. Skerka

Date Published: 11th May 2020

Publication Type: Not specified

Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression

Abstract

ABSTRACT:

Authors: Sebastian Müller, Clara Baldin, Marco Groth, Reinhard Guthke, Olaf Kniemeyer, Axel A Brakhage, Vito Valiante

Date Published: 2nd Oct 2012

Publication Type: Not specified

Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant

Abstract (Expand)

Following antifungal treatment, Candida albicans, and other human pathogenic fungi can undergo microevolution, which leads to the emergence of drug resistance. However, the capacity for microevolutionary … adaptation of fungi goes beyond the development of resistance against antifungals. Here we used an experimental microevolution approach to show that one of the central pathogenicity mechanisms of C. albicans, the yeast-to-hyphae transition, can be subject to experimental evolution. The C. albicans cph1Delta/efg1Delta mutant is nonfilamentous, as central signaling pathways linking environmental cues to hyphal formation are disrupted. We subjected this mutant to constant selection pressure in the hostile environment of the macrophage phagosome. In a comparatively short time-frame, the mutant evolved the ability to escape macrophages by filamentation. In addition, the evolved mutant exhibited hyper-virulence in a murine infection model and an altered cell wall composition compared to the cph1Delta/efg1Delta strain. Moreover, the transcriptional regulation of hyphae-associated, and other pathogenicity-related genes became re-responsive to environmental cues in the evolved strain. We went on to identify the causative missense mutation via whole genome- and transcriptome-sequencing: a single nucleotide exchange took place within SSN3 that encodes a component of the Cdk8 module of the Mediator complex, which links transcription factors with the general transcription machinery. This mutation was responsible for the reconnection of the hyphal growth program with environmental signals in the evolved strain and was sufficient to bypass Efg1/Cph1-dependent filamentation. These data demonstrate that even central transcriptional networks can be remodeled very quickly under appropriate selection pressure.

Authors: A. Wartenberg, , R. Martin, M. Schreiner, F. Horn, , S. Jenull, , K. Kuchler, , , A. Forche, C. d'Enfert, S. Brunke,

Date Published: 4th Dec 2014

Publication Type: Not specified

The transcriptional stress response of Candida albicans to weak organic acids.

Abstract (Expand)

Candida albicans is the most important fungal pathogen of humans, causing severe infections, especially in nosocomial and immunocompromised settings. However, it is also the most prevalent fungus of … the normal human microbiome, where it shares its habitat with hundreds of trillions of other microbial cells. Despite weak organic acids (WOAs) being among the most abundant metabolites produced by bacterial microbiota, little is known about their effect on C. albicans. Here we used a sequencing-based profiling strategy to systematically investigate the transcriptional stress response of C. albicans to lactic, acetic, propionic, and butyric acid at several time points after treatment. Our data reveal a complex transcriptional response, with individual WOAs triggering unique gene expression profiles and with important differences between acute and chronic exposure. Despite these dissimilarities, we found significant overlaps between the gene expression changes induced by each WOA, which led us to uncover a core transcriptional response that was largely unrelated to other previously published C. albicans transcriptional stress responses. Genes commonly up-regulated by WOAs were enriched in several iron transporters, which was associated with an overall decrease in intracellular iron concentrations. Moreover, chronic exposure to any WOA lead to down-regulation of RNA synthesis and ribosome biogenesis genes, which resulted in significant reduction of total RNA levels and of ribosomal RNA in particular. In conclusion, this study suggests that gastrointestinal microbiota might directly influence C. albicans physiology via production of WOAs, with possible implications of how this fungus interacts with its host in both health and disease.

Authors: F. Cottier, A. S. Tan, J. Chen, J. Lum, F. Zolezzi, M. Poidinger, N. Pavelka

Date Published: 1st Feb 2015

Publication Type: Not specified

Template_RNA-seq_V1.9
No description specified

Source: Specimen (String) *, Source: Material Type (String) , Source: Organism (String) , Source: Strain or Line (String) , Source: Organism Part (String) , Source: OrganismStatus (String) , Source: Number of fungal organisms (Integer) , Source: Unit for number of fungi (String) , Source: Sex (e.g. for mice) (String) , Source: Age (Real number) , Source: Age Time Unit (String) , Source: Sampling Time Point (Real number) , Source: Sampling Time Point Unit (String) , Source: Temperature (Real number) , Source: Temperature Unit (String) , Source: pH (Real number) , Source: Atmosphere (String) , Source: Compound (String) , Source: Media (String) , Source: Nutrients (String) , Source: Storage Protocol (String) , Source: Storage Date (Date) , Source: Storage Location (String) , RNA Extraction: Extraction Protocol (String) , RNA Extraction: Extract Name (String) , RNA Extraction: 260/280 (Real number) , RNA Extraction: 230/280 (Real number) , RNA Extraction: RIN/RNA integrity number (Real number) , RNA Extraction: Concentration (Real number) , RNA Extraction: Concentration Unit (String) , RNA Extraction: Volume (Real number) , RNA Extraction: Volume Unit (String) , RNA Extraction: Extraction Kit (String) , RNA Extraction: Material Type (String) , RNA Extraction: Extraction Date (Date) , RNA Extraction: Storage Protocol (String) , RNA Extraction: Storage Date (Date) , RNA Extraction: Storage Location (String) , Sequencing: Sequencing Protocol (String) , Sequencing: Assay Name (String) , Sequencing: Sequencing Performer (String) , Sequencing: Technology Type (String) , Sequencing: Read Length (Integer) , Sequencing: Sequencing Instrument (String) , Sequencing: Library Source (String) , Sequencing: Library Strategy (Text) , Sequencing: Library Selection (String) , Sequencing: Library Layout (String) , Sequencing: Sequencing Date (Date) , Sequencing: Storage Protocol (String) , Sequencing: Storage Date (Date) , Sequencing: Storage Location (String) , Sequencing: Data File (Text)

RNA-seq

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