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. 2017 Apr 26;6(4):e24.
doi: 10.1038/emi.2017.9.

Zika virus infection reprograms global transcription of host cells to allow sustained infection

Affiliations

Zika virus infection reprograms global transcription of host cells to allow sustained infection

Shashi Kant Tiwari et al. Emerg Microbes Infect. .

Abstract

Zika virus (ZIKV) is an emerging virus causally linked to neurological disorders, including congenital microcephaly and Guillain-Barré syndrome. There are currently no targeted therapies for ZIKV infection. To identify novel antiviral targets and to elucidate the mechanisms by which ZIKV exploits the host cell machinery to support sustained replication, we analyzed the transcriptomic landscape of human microglia, fibroblast, embryonic kidney and monocyte-derived macrophage cell lines before and after ZIKV infection. The four cell types differed in their susceptibility to ZIKV infection, consistent with differences in their expression of viral response genes before infection. Clustering and network analyses of genes differentially expressed after ZIKV infection revealed changes related to the adaptive immune system, angiogenesis and host metabolic processes that are conducive to sustained viral production. Genes related to the adaptive immune response were downregulated in microglia cells, suggesting that ZIKV effectively evades the immune response after reaching the central nervous system. Like other viruses, ZIKV diverts host cell resources and reprograms the metabolic machinery to support RNA metabolism, ATP production and glycolysis. Consistent with these transcriptomic analyses, nucleoside metabolic inhibitors abrogated ZIKV replication in microglia cells.

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Figures

Figure 1
Figure 1
Variable ZIKV infection and replication levels in different cell types. (AD) Immunohistochemistry of ZIKV gene expression in microglial, fibroblast (BJ), kidney (293FT) and macrophage (THP-1) cell lines at 24 hpi. Cells were stained with anti-flavivirus envelope protein (ZIKVE), and nuclei were visualized with Hoechst 33258 (Invitrogen). (E) ZIKV replication assessed by one-step quantitative PCR with reverse transcription analysis of viral supernatants at the indicated times post infection. Data are presented as the mean±SEM of n=3. *P<0.05, **P<0.01, ***P<0.001; ns, not significant by two-way analysis of variance. See also Supplementary Figure S1. Zika virus, ZIKV.
Figure 2
Figure 2
Changes in the transcriptional landscape following ZIKV infection. (AD) Circos plots of transcriptional changes in microglia (A), BJ (B), 293FT (C) and THP-1-derived macrophages (D) at 24 hpi. The outer circles (blue, brown, green and magenta) represent the expression levels of the transcripts before infection. The inner circles represent the differentially expressed genes, with the size of the lines indicating the fold change in expression. Genes upregulated and downregulated by ZIKV infection are shown in red and blue, respectively. (E) Circos plot showing differentially expressed genes in all four cell types. The number of differentially expressed genes and the magnitude of the expression change are inversely correlated with ZIKV expression. Upregulated genes are in red and downregulated genes are in blue. Outer to inner circles: THP-1, 293FT, BJ and microglia. Zika virus, ZIKV.
Figure 3
Figure 3
Cell-type-specific differences in steady-state expression of viral response genes reveal potential antiviral targets. (A) Hierarchical clustering of genes associated with ‘response to virus' (top) and the fold change in expression of the same genes at 24 hpi (bottom). Left scale bar: 0:10 represents gene expression log2 (RPKM+1) for all cell lines. Right scale bar: −2:2 represents fold change in gene expressed between mock-treated and ZIKV-infected cells. Also see Supplementary Table S1. (B) Pre-infection expression levels of genes associated with ‘response to virus.' (C) Hierarchical clustering of genes associated with ‘cell surface' (top) and their associated fold change in expression following infection (bottom). Also see Supplementary Table S3. (D) Differential gene expression of cell surface proteins and receptors involved in cell activation, immune response and cell surface signaling in THP-1-derived macrophages. See also Supplementary Figure S2. (E) Gene ontology analysis of cell surface genes highly expressed specifically in THP-1. Zika virus, ZIKV.
Figure 4
Figure 4
Analysis of differentially expressed genes post ZIKV infection identifies key pathways exploited by ZIKV. (A) Hierarchical clustering of differentially expressed genes following ZIKV infection, showing cell-type-specific transcriptional changes. Genes displayed have fold changes of >1.4 and P<0.05 in at least one cell type. The vertical bar to the right indicates the differentially expressed gene clusters described by color in the text. Also see Supplementary Table S4. (B) Interactome of differentially expressed genes across all cell types. (C) Gene ontology analysis of ‘red cluster' genes, which are upregulated in microglia and THP-1-derived macrophages. (D) Gene ontology analysis of ‘yellow cluster' genes, which are mostly downregulated in microglia and THP-1-derived macrophages. (E) Analysis of ‘green cluster' genes, which are upregulated only in THP-1. (F) Analysis of ‘magenta cluster' genes, which are upregulated in 293FT and THP-1-derived macrophages. (G) Analysis of ‘blue cluster' genes, which are only upregulated in microglia cells. See also Supplementary Figure S3. Zika virus, ZIKV.
Figure 5
Figure 5
Nucleoside metabolic inhibitors attenuate ZIKV replication. (A) ZIKV replication assessed by RT-qPCR 48 hpi in mock, ZIKV only, ZIKV plus 1 μM floxuridine (FUDX1) or ZIKV plus 10 μM floxuridine (FUDX10)-treated microglia. Data are presented as the mean±sem of n=3. *P<0.05, **P<0.01 by t-test. (B) Immunohistochemistry of anti-flavivirus envelope protein (ZIKVE) expression in mock, ZIKV only, ZIKV plus FUDX1 or ZIKV plus FUDX10-treated microglia. (C) ZIKV replication assessed by RT-qPCR analysis 48 hpi in mock, ZIKV only, ZIKV plus 1 μM flurouracil (FU1) or ZIKV plus 10 μM flurouracil (FU10)-treated microglia. Data are presented as the mean±SEM of n=3. *P<0.05, **P<0.01 by t-test. (D) Immunohistochemistry of ZIKVE expression in mock, ZIKV only, ZIKV plus 1 μM FU1 or ZIKV plus FU10-treated microglia. Quantitative PCR with reverse transcription, RT-qPCR; Zika virus, ZIKV.

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