Complex modulation of the Aedes aegypti transcriptome in response to dengue virus infection

Abstract

Dengue fever is the most important arboviral disease world-wide, with Aedes aegypti being the major vector. Interactions between the mosquito host and dengue viruses (DENV) are complex and vector competence varies among geographically-distinct Ae. aegypti populations. Additionally, dengue is caused by four antigenically-distinct viral serotypes (DENV1-4), each with multiple genotypes. Each virus genotype interacts differently with vertebrate and invertebrate hosts. Analyses of alterations in mosquito transcriptional profiles during DENV infection are expected to provide the basis for identifying networks of genes involved in responses to viruses and contribute to the molecular-genetic understanding of vector competence. In addition, this knowledge is anticipated to support the development of novel disease-control strategies. RNA-seq technology was used to assess genome-wide changes in transcript abundance at 1, 4 and 14 days following DENV2 infection in carcasses, midguts and salivary glands of the Ae. aegypti Chetumal strain. DENV2 affected the expression of 397 Ae. aegypti genes, most of which were down-regulated by viral infection. Differential accumulation of transcripts was mainly tissue- and time-specific. Comparisons of our data with other published reports reveal conservation of functional classes, but limited concordance of specific mosquito genes responsive to DENV2 infection. These results indicate the necessity of additional studies of mosquito-DENV interactions, specifically those focused on recently-derived mosquito strains with multiple dengue virus serotypes and genotypes.

Figure 1. Numbers of genes whose transcripts accumulate differentially in response to dengue virus infection.

(A) Venn diagrams with the number of genes whose transcripts accumulate differentially in response to dengue virus infection in carcasses (C), midguts (M) and salivary glands (SG) at 1, 4 and 14 days post infection (dpi). (B) Venn diagrams with the number of genes whose transcripts accumulate differentially in response to dengue virus infection in carcasses (C) and midguts (M) at different time-points.

Figure 2. Functional categories of genes whose transcripts accumulate differentially in response to dengue virus infection in multiple tissues and times during infection.

The functional categories for genes whose transcripts accumulate differentially in response to dengue virus infection are shown for each time point and tissue. The number of genes is shown in parentheses in each figure. Abbreviations for functional categories are: unknown (UNK), metabolism (MET), immunity (IMM), cytoskeleton, cell wall, cell motility and extracellular structures (C-CW-CM-ES), post-translational modification, protein turnover, chaperone (PM-PT-C), signal transduction (ST), proteolysis (PROT), oxidoreductase activity (REDOX), transcription and translation (TT), diverse (DIV), transport (TR), cell-cycle (CC), energy production and conversion (EPC), chromatin structure and dynamics (CSD). All other abbreviations are the same as Figure 1.

Figure 3. Genes whose transcripts accumulate differentially in carcasses throughout the course of dengue infection.

FPKM values (colored bars) and Log2-fold changes in accumulation levels (filled triangles) are plotted on the left and right y-axes, respectively. Individual genes are listed by Ensembl Gene ID numbers and represented by the numerals on the x-axis. Abbreviations for the functional categories of each gene are the same as Figure 2.

Figure 4. Examples of CRE discovery.

MEME analysis of nine genes with FPKM_DENVI≥100 in carcasses and salivary glands at 14 dpi. These genes also were identified with transcripts exhibiting significant differential accumulation in analyses of salivary gland samples of the Liverpool strain infected with DEV2 Thailand 16881 . Colored boxes represent individual putative CREs and their locations in promoters of each gene. Red and blue arrows adjacent to Ensembl Gene ID indicate those genes whose transcripts were detected previously as more or less abundant following DENV infection . Distances in base-pairs are provided below the schematic of each gene.