Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach

Abstract

Background: Aspergillus fumigatus (Af) is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic background. The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus (Af) using an RNAseq approach in CC lines and hepatic gene expression.

Methods: We studied 31 male mice from 25 CC lines at 8 weeks old; the mice were infected with Af. Liver tissues were extracted from these mice 5 days post-infection, and next-generation RNA-sequencing (RNAseq) was performed. The GENE-E analysis platform was used to generate a clustered heat map matrix.

Results: Significant variation in body weight changes between CC lines was observed. Hepatic gene expression revealed 12 top prioritized candidate genes differentially expressed in resistant versus susceptible mice based on body weight changes. Interestingly, three candidate genes are located within genomic intervals of the previously mapped quantitative trait loci (QTL), including Gm16270 and Stox1 on chromosome 10 and Gm11033 on chromosome 8.

Conclusions: Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af. As a next step, eQTL analysis will be performed for our RNA-Seq data. Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.

Keywords: RNA‐Seq; aspergillus fumigatus infection; collaborative cross (CC) mice; gene expression profile; gene‐network; host susceptibility; quantitative trait loci (QTL) mapping.

FIGURE 1

Mean body weight status in grams (gr) for different CC lines during 5 days of infection with Aspergillus fumigatus (Af). The x‐axis shows the two time points (time 0, time 5th day) post‐infection, and the y‐axis shows the body weight status in grams (gr) for the different CC lines during the 5 days of infection. One‐way ANOVA was performed for statistical analysis, p < 0.05.

FIGURE 2

Comparison of body weight changes (Δ delta body weight) in grams (gr) of the CC lines after the period of 5 days infection (Δ0–5); The x‐axis represents the different assessed CC lines, and the y‐axis represents ∆ body weight in grams of all the 25 CC lines, and the mean for the whole lines.

FIGURE 3

The heat map presents expression levels with the lowest falls discovery rate (FDR) values in liver tissues. Genomic data were obtained from the 31 mice from the 25 different CC lines. High and low gene expression levels are in red and blue, respectively. Each individual (a column) is annotated with the CC strain designation. The names of several genes are shown on right. The percentage weight loss of each individual is indicated as a bar plot (top).

FIGURE 4

The kynurenine pathway is a significant pathway for tryptophan (TRY) catabolism. TRY in the central nervous system (CNS) resembles a protein precursor, the only one that can pass the blood–brain barrier (BBB).