Single-cell transcriptional dynamics of flavivirus infection

Abstract

Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.

ISG15/USP18/STAT2 is a molecular hub regulating autocrine IFN I-mediated control of Dengue and Zika virus replication

“…We used t-Distributed Stochastic Neighbor Embedding (tSNE) analysis to visualize cell-to-cell relationships in space of reduced dimensionality. As reported previously (Zanini et al, 2018a(Zanini et al, , 2018b, global cellular mRNA expression profiling was not sufficient to separate infected or bystander from uninfected cells, suggesting a high variability of gene expression in these samples ( Figure 1A and S1A). As IFN-I are key elements in controlling infection, we filtered the results of the differential gene expression analysis using the gene ontology (GO) term for "type one interferon".…”

“…The cell is a fundamental unit for viral infection control and developments in single-cell sequencing technology have enabled examination of hostpathogen interactions in great detail. Recently, Zanini and colleagues generated single-cell RNA sequencing of two independent data sets of DVinfected human cells (PBMCs and the HuH7 hepatoma cell line) (Zanini et al, 2018a(Zanini et al, , 2018b. We re-analyzed available single-cell transcriptomic data dividing cells into three categories: uninfected, infected and bystander.…”

Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing

“…Of note, in the special case of positivesense ssRNA viruses, our approach is not applicable due to the lack of polyadenylated transcriptome (e.g., Zika, dengue, and yellow fever viruses) or the polyadenylated genome (e.g., foot-and-mouth disease virus, rubella, and severe acute respiratory syndrome). Tailored technologies have been developed for this specific case (e.g., Zanini et al, 2018). Our dual-transcriptome approach shares with these technologies the challenge of distinguishing intracellular viral transcription from exogenous acquisition (by phagocytosis) of infected cells.…”

“…For example, while epithelial cells are known to be the main targets of the influenza virus, several studies have documented that other cell types, such as endothelial cells, natural killer (NK) cells, macrophages, and dendritic cells (DCs), are also susceptible to the influenza virus, with potential implications of intracellular infection for their functionality (Manicassamy et al, 2010;McFadden et al, 2009). Complexity may also be related to a wide range of viral transcriptional states within the infected cells (Russell et al, 2018;Xin et al, 2018;Zanini et al, 2018), as well as to the heterogeneity of host-response states (Avraham et al, 2015). Another complication may be attributable to the dual role of the metabolic machinery in supporting the host while also limiting the energetic demands of the viral life cycle (Jovanovic et al, 2015;Kissig et al, 2017).…”

Prediction of SARS-CoV interaction with host proteins during lung aging reveals a potential role for TRIB3 in COVID-19

“…Additionally, TRIB3 negatively regulates the entry step of the HCV life cycle and propagation 22 and thus may constitute a common protective host factor for other positive-sense single-strand RNA viruses. TRIB3 is also one of the unfolded protein response (UPR)-related genes with the strongest positive correlation with the intracellular abundance of the flavivirus dengue and Zika 23 . Considering the need for drugs to treat COVID-19, the α -hydroxylinoleic acid (ABTL0812) induces the expression of TRIB3 by inhibiting the PI3K/AKT/mTOR axis and promoting autophagy cell death in cancer 24 .…”