Abstract
Candida albicans adaptation to the host requires a profound reprogramming of the fungal transcriptome as compared to in vitro laboratory conditions. A detailed knowledge of the C. albicans transcriptome during the infection process is necessary in order to understand which of the fungal genes are important for host adaptation. Such genes could be thought of as potential targets for antifungal therapy. The acquisition of the C. albicans transcriptome is, however, technically challenging due to the low proportion of fungal RNA in host tissues. Two emerging technologies were used recently to circumvent this problem. One consists of the detection of low abundance fungal RNA using capture and reporter gene probes which is followed by emission and quantification of resulting fluorescent signals (nanoString). The other is based first on the capture of fungal RNA by short biotinylated oligonucleotide baits covering the C. albicans ORFome permitting fungal RNA purification. Next, the enriched fungal RNA is amplified and subjected to RNA sequencing (RNA-seq). Here we detail these two transcriptome approaches and discuss their advantages and limitations and future perspectives in microbial transcriptomics from host material.
Highlights
Fungal pathogens of mammals are able to live and proliferate in a wide range of host body sites including skin surfaces and mucosa, and internal organs
On the opposite to C. neoformans and A. fumigatus cells which can be collected from host fluids to significant numbers, C. albicans sampling from the host is more problematic since C. albicans cells in the host are associated to host tissues or embedded in organs
The first 250 nucleotides of each gene were not covered in the bait design, resulting in an average of nine probes for each ORF. The use of this capture system on RNA obtained from infected host tissues resulted in enrichments in the proportion of C. albicans transcripts of more than 500fold and in RNA sequencing (RNA-seq) libraries containing more than 50% of fungal transcripts
Summary
A detailed knowledge of the C. albicans transcriptome during the infection process is necessary in order to understand which of the fungal genes are important for host adaptation. Such genes could be thought of as potential targets for antifungal therapy. One consists of the detection of low abundance fungal RNA using capture and reporter gene probes which is followed by emission and quantification of resulting fluorescent signals (nanoString). The enriched fungal RNA is amplified and subjected to RNA sequencing (RNA-seq). We detail these two transcriptome approaches and discuss their advantages and limitations and future perspectives in microbial transcriptomics from host material
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