Host Transcriptional Response to Ebola Virus Infection

Abstract

Ebola virus disease (EVD) is a serious illness that causes severe disease in humans and non-human primates (NHPs) and has mortality rates up to 90%. EVD is caused by the Ebolavirus and currently there are no licensed therapeutics or vaccines to treat EVD. Due to its high mortality rates and potential as a bioterrorist weapon, a better understanding of the disease is of high priority. Multiparametric analysis techniques allow for a more complete understanding of a disease and the host response. Analysis of RNA species present in a sample can lead to a greater understanding of activation or suppression of different states of the immune response. Transcriptomic analyses such as microarrays and RNA-Sequencing (RNA-Seq) have been important tools to better understand the global gene expression response to EVD. In this review, we outline the current knowledge gained by transcriptomic analysis of EVD.

Keywords: Ebola virus disease; RNA-Seq; host response; immune response; microarray; transcriptomic.

Figure 1

Suppression of the transcriptional response to EBOV infection in immortalized cell lines. Illustration depicts the currently understood mechanism of virus–host antagonism following EBOV entry into the cell. Upon viral uncoating, the virus releases two important viral proteins, VP35 and VP24 (represented in red). VP35 is capable of blocking activation of and signaling through the RIG-I pattern receptor, maintaining inhibitor of nuclear factor kappa B kinase subunit epsilon (IKKE)/TANK Binding Kinase 1 (TBK1) in an inactive state (host proteins are illustrated in green, with activating phosphorylation events depicted in yellow). This prevents the phosphorylation and activation of interferon response factor 3 (IRF3) and thereby the transcription of interferon (IFN) beta and IRF3-responsive interferon stimulated genes (ISGs). VP24 acts downstream of signal transducer and activator of transcription (STAT) protein phosphorylation by janus kinase (JAK) to inhibit the translocation of STATs to the nucleus, thereby inhibiting interferon signaling. Mutations in VP35 or VP24 compromise the host antagonism of each protein and result in the activation of ISG transcription following EBOV infection. Depicted in blue is the inhibition of coagulation genes that is seen following EBOV infection. Question marks signify that the mechanism by which this suppression occurs is unknown.

Figure 2

Virus–host antagonism following EBOV infection of macrophages or dendritic cells. Left panel illustrates the response to EBOV entry and attachment in macrophages. Upon attachment, activation of tool like receptor 4 (TLR-4) and nuclear factor kappa B (NF-$\kappa$B) by the entry process lead to the induction of inflammatory transcripts. IRF3/IFN-induced genes are also induced in macrophage-infected cells, suggesting that the function of VP24 and VP35 as viral antagonists of these signaling pathways is compromised or that other signaling pathways are activated. The right-hand panel illustrates the interaction of EBOV and the host-response in dendritic cells. Similar to what is seen in many immortalized cell lines, VP35 will act as a strong inhibitor of IRF-3 phosphorylation blocking interferon and ISG transcription. Also, VP24 will act as an inhibitor of translocation of pSTAT1/2 to the nucleus further blocking interferon transcription.

Figure 3

The host transcriptional response to EBOV infection in mouse liver and spleen. In the liver (left), all mice challenged with EBOV show transcriptional changes. Animals that succumb experience a peak point of transcriptional activity at 48 h post-infection (HPI.). Genes are enriched for transcripts associated with loss of vascular permeability. Surviving mice do not experience a peak of transcriptional activity until 72 HPI and do not induce genes associated with the breakdown of the vascular layers. In the spleen (right), all animals challenged with EBOV mount a transcriptional response to infection. In animals that will succumb to disease, peak transcriptional activity is observed at 72 HPI. These transcripts are associated with a strong induction of ISGs, the inflammatory response, and evidence of neutrophil infiltration. In animals that survive, there are lower levels of transcriptional activity throughout infection. There is moderate up-regulation of ISGs and a weak inflammatory response.

Figure 4

The host transcriptional response to EBOV challenge in NHPs. The illustration shows three distinct stages of transcriptional activation seen in peripheral blood mononuclear cells (PBMCs) following EBOV infection of NHPs. The top half (above the black line) shows the likely viral progression of EBOV from the infection of initial target cells (green phase) to replication in the spleen and liver (blue phase) and finally dissemination into secondary organs (red phase). The bottom panels illustrate the transcriptional activity of different gene families during this progression. The earliest phase of transcriptional activity (0–2 days post-infection (DPI)), in the green box, is the silent phase where very little if any transcriptional activity is present in the PBMCs. During this phase, the virus has initiated infection in primary cell targets. As the virus moves to its primary organs of infection, a robust early phase of transcriptional activity is observed (2–4 DPI). Most notable in this phase is the increase in ISGs. This ISG induction is closely followed by the induction of cytokine genes. Finally, as the virus begins to disseminate through the whole body through the blood (viremia) and begins to infect secondary organ targets, the transcriptional activity enters the late phase characterized by the induction of many pro-inflammatory genes, pro-apoptotic markers, and neutrophil markers in PBMCs.