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. 2018 Oct 24;3(5):e00445-18.
doi: 10.1128/mSphere.00445-18.

Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways

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Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways

Rhys A Farrer et al. mSphere. .

Abstract

Cryptococcus gattii is a pathogenic yeast of humans and other animals which causes disease predominantly in immunocompetent hosts. Infection begins when aerosolized yeast or spores enter the body, triggering an immune response, including engulfment by macrophages. To understand the early transcriptional signals in both the yeast and its mammalian host, we performed a time-course dual-transcriptome sequencing (RNA-seq) experiment for four lineages of C. gattii (lineages VGI to IV) interacting with mouse macrophages at 1, 3, and 6 h postinfection. Comparisons of in vitro to ex vivo gene expression levels indicated that lineage VGII is transcriptionally divergent from non-VGII lineages, including differential expression of genes involved in capsule synthesis, capsule attachment, and ergosterol production. Several paralogous genes demonstrated subfunctionalization between lineages, including upregulation of capsule biosynthesis-related gene CAP2 and downregulation of CAP1 in VGIII. Isolates also compensate for lineage-specific gene losses by overexpression of genetically similar paralogs, including overexpression of capsule gene CAS3 in VGIV, which have lost the CAS31 gene. Differential expression of one in five C. gattii genes was detected following coincubation with mouse macrophages; all isolates showed high induction of oxidative-reduction functions and downregulation of capsule attachment genes. We also found that VGII switches expression of two laccase paralogs (from LAC1 to LAC2) during coincubation of macrophages. Finally, we found that mouse macrophages respond to all four lineages of C. gattii by upregulating FosB/Jun/Egr1 regulatory proteins at early time points. This report highlights the evolutionary breadth of expression profiles among the lineages of C. gattii and the diversity of transcriptional responses at this host-pathogen interface.IMPORTANCE The transcriptional profiles of related pathogens and their responses to host-induced stresses underpin their pathogenicity. Expression differences between related pathogens during host interaction can indicate when and how these genes contribute to virulence, ultimately informing new and improved treatment strategies for those diseases. In this paper, we compare the transcriptional profiles of five isolates representing four lineages of C. gattii in rich media. Our analyses identified key processes, including those involving cell capsule, ergosterol production, and melanin, that are differentially expressed between lineages, and we found that VGII has the most distinct profile in terms of numbers of differentially expressed genes. All lineages have also undergone subfunctionalization for several paralogs, including capsule biosynthesis and attachment genes. Most genes appeared downregulated during coincubation with macrophages, with the largest decrease observed for capsule attachment genes, which appeared to be coordinated with a stress response, as all lineages also upregulated oxidative stress response genes. Furthermore, VGII upregulated many genes that are linked to ergosterol biosynthesis and switched from expression of the laccase LAC1 to expression of LAC2 ex vivo Finally, we saw a pronounced increase in the FosB/Jun/Egr1 regulatory proteins at early time points in bone marrow-derived macrophages, marking a role in the host response to C. gattii This work highlights the dynamic roles of key C. gattii virulence genes in response to macrophages.

Keywords: Cryptococcus; capsule; ergosterol; host response; host-pathogen interactions; laccase; mRNA.

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Figures

FIG 1
FIG 1
Heat maps of the Log2 fold change in the trimmed mean of M-values (TMM) normalized fragments per kilobase of transcript per million mapped reads (FPKM) of C. gattii (a) and mouse BMDM (b) transcripts per sample.
FIG 2
FIG 2
The number of Cryptococcus gattii genes up- and downregulated between lineages in vitro (a) and between time points (b) and principal-component analysis (PCA) of differentially expressed genes in vitro (c) and between time points (d) and the locations of those genes in their genomes (synteny plotted using Synima [48]) alongside a phylogenetic tree constructed with RAxML (GTRCAT) with 1,000-bootstrap support (shown as asterisks) (e). Genes are considered differentially expressed where the FDR P value is <0.001 and the TMM FPKM is greater than 4-fold. Colored boxes show the genomic locations of differentially expressed genes (DEGs) with colors corresponding to panels a and b: in vitro, yellow; t0 versus another time point, blue; t1 versus another time point, red; t3 versus another time point, green; t6 versus another time point, purple.
FIG 3
FIG 3
Bar charts showing mean expression (TMM FPKM) of ergosterol, capsular biosynthesis, capsular attachment, and laccase genes differentially expressed between the five isolates of Cryptococcus gattii in vitro. Red, significantly (Sig.) upregulated; blue, Sig. downregulated. Genes are considered differentially expressed (D.E.) where the FDR P value is <0.001 and the TMM FPKM is greater than 4-fold. Error bars show the range of TMM FPKM values in comparisons between the two replicates.
FIG 4
FIG 4
Bar charts showing mean expression (TMM FPKM) of differentially expressed ergosterol, capsular biosynthesis, capsular attachment and laccase genes between the five isolates of Cryptococcus gattii at each time point (t0 = in vitro, t1 = 1-h w/BMDMs, t3 = 3 h w/BMDMs, and t6 = 6 h w/BMDMs). Red, significantly upregulated; blue, significantly downregulated. Genes are considered differentially expressed where FDR P value < 0.001 and greater than 4-fold TMM FPKM. Error bars show the range of TMM FPKM values in comparisons between the two replicates. Glucan, glucan 1,3-β-glucosidase.
FIG 5
FIG 5
A bar chart showing the number of mouse genes up- and downregulated by each of the five isolates of C. gattii compared with growth without yeast. Where the same gene was found in multiple pairwise comparisons, it is included only once in the redundant categories (applicable only for the grouped category). Positive values indicate genes that were upregulated in that isolate/lineage compared with others, while negative values (below zero) indicate genes that were downregulated in that isolate/lineage compared with others. Genes are considered differentially expressed where FDR P value are <0.001 and TMM FPKM values are greater than 4-fold.

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