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Investigation of Aspergillus fumigatus biofilm formation by various "omics" approaches.

Muszkieta L, Beauvais A, Pähtz V, Gibbons JG, Anton Leberre V, Beau R, Shibuya K, Rokas A, Francois JM, Kniemeyer O, Brakhage AA, Latgé JP - Front Microbiol (2013)

Bottom Line: In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF).This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment.Recent works have shown that the fungus in this aerial grown BF-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence.

View Article: PubMed Central - PubMed

Affiliation: Unité des Aspergillus, Institut Pasteur Paris Cedex, France.

ABSTRACT
In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF). This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment. This extracellular matrix is absent in fungal colonies grown under classical liquid shake conditions (PL), which were historically used to understand A. fumigatus pathobiology. Recent works have shown that the fungus in this aerial grown BF-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence. These differences in pathological and physiological characteristics between BF and liquid shake conditions suggest that the PL condition is a poor in vitro disease model. In the laboratory, A. fumigatus mycelium embedded by the extracellular matrix can be produced in vitro in aerial condition using an agar-based medium. To provide a global and accurate understanding of A. fumigatus in vitro BF growth, we utilized microarray, RNA-sequencing, and proteomic analysis to compare the global gene and protein expression profiles of A. fumigatus grown under BF and PL conditions. In this review, we will present the different signatures obtained with these three "omics" methods. We will discuss the advantages and limitations of each method and their complementarity.

No MeSH data available.


Related in: MedlinePlus

Identification of the differentially expressed genes common to both transcriptomic methods. (A) Comparison of the up regulated genes obtained with microarray and RNA-sequencing analysis in the biofilm. (B) Comparison of the down regulated genes obtained with microarray and RNA-sequencing analysis in the biofilm. (C) Comparison of the fold change obtained with microarray and RNA-sequencing analysis.
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Figure 2: Identification of the differentially expressed genes common to both transcriptomic methods. (A) Comparison of the up regulated genes obtained with microarray and RNA-sequencing analysis in the biofilm. (B) Comparison of the down regulated genes obtained with microarray and RNA-sequencing analysis in the biofilm. (C) Comparison of the fold change obtained with microarray and RNA-sequencing analysis.

Mentions: In spite of these discrepancies, it was observed that among the 193 up regulated genes identified by microarrays, 119 were also up regulated in the RNA-sequencing data (Figure 2A). Among the 169 down regulated genes identified in the microarrays only 56 were shown to be down regulated in the RNA-sequencing analysis (Figure 2B). Thus, ~49% of the differentially expressed genes identified with microarrays were also retrieved in the RNA-sequencing data with a positive correlation of p = 0.82 (Pearson correlation) (Figure 2C). Some of the common differentially expressed genes found in both transcriptomic methods are discussed below (Table 4).


Investigation of Aspergillus fumigatus biofilm formation by various "omics" approaches.

Muszkieta L, Beauvais A, Pähtz V, Gibbons JG, Anton Leberre V, Beau R, Shibuya K, Rokas A, Francois JM, Kniemeyer O, Brakhage AA, Latgé JP - Front Microbiol (2013)

Identification of the differentially expressed genes common to both transcriptomic methods. (A) Comparison of the up regulated genes obtained with microarray and RNA-sequencing analysis in the biofilm. (B) Comparison of the down regulated genes obtained with microarray and RNA-sequencing analysis in the biofilm. (C) Comparison of the fold change obtained with microarray and RNA-sequencing analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569664&req=5

Figure 2: Identification of the differentially expressed genes common to both transcriptomic methods. (A) Comparison of the up regulated genes obtained with microarray and RNA-sequencing analysis in the biofilm. (B) Comparison of the down regulated genes obtained with microarray and RNA-sequencing analysis in the biofilm. (C) Comparison of the fold change obtained with microarray and RNA-sequencing analysis.
Mentions: In spite of these discrepancies, it was observed that among the 193 up regulated genes identified by microarrays, 119 were also up regulated in the RNA-sequencing data (Figure 2A). Among the 169 down regulated genes identified in the microarrays only 56 were shown to be down regulated in the RNA-sequencing analysis (Figure 2B). Thus, ~49% of the differentially expressed genes identified with microarrays were also retrieved in the RNA-sequencing data with a positive correlation of p = 0.82 (Pearson correlation) (Figure 2C). Some of the common differentially expressed genes found in both transcriptomic methods are discussed below (Table 4).

Bottom Line: In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF).This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment.Recent works have shown that the fungus in this aerial grown BF-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence.

View Article: PubMed Central - PubMed

Affiliation: Unité des Aspergillus, Institut Pasteur Paris Cedex, France.

ABSTRACT
In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF). This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment. This extracellular matrix is absent in fungal colonies grown under classical liquid shake conditions (PL), which were historically used to understand A. fumigatus pathobiology. Recent works have shown that the fungus in this aerial grown BF-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence. These differences in pathological and physiological characteristics between BF and liquid shake conditions suggest that the PL condition is a poor in vitro disease model. In the laboratory, A. fumigatus mycelium embedded by the extracellular matrix can be produced in vitro in aerial condition using an agar-based medium. To provide a global and accurate understanding of A. fumigatus in vitro BF growth, we utilized microarray, RNA-sequencing, and proteomic analysis to compare the global gene and protein expression profiles of A. fumigatus grown under BF and PL conditions. In this review, we will present the different signatures obtained with these three "omics" methods. We will discuss the advantages and limitations of each method and their complementarity.

No MeSH data available.


Related in: MedlinePlus