Figure 1. Genome-wide Integrative Analysis of miRNAs in ZIKV-Infected hNSCs.

(A) Experimental design. hNSCs were infected with ZIKV MR766 or Paraiba for 3 days at an MOI of 1. Total RNA was analyzed by RNA-seq or miRNA-seq to identify miRNA-regulated networks of genes implicated in ZIKV pathogenesis. DE, differentially expressed.

(B) qRT-PCR analysis of ZIKV MR766 and ZIKV Paraiba copy number on days 1, 2, and 3 post-inoculation of hNSCs at an MOI of 1. Data are means ± SEM of biological triplicates.

(C) Fluorescence immunostaining of ZIKV envelope protein (ZIKVE) in hNSCs on days 1, 2, and 3 post-infection with ZIKV MR766 or Paraiba at an MOI of 1. Nuclei were stained with DAPI. Scale bar, 100 μm.

(D) Venn diagram of differentially expressed genes in ZIKV MR766- and Paraiba-infected hNSCs at 3 days post-infection at an MOI of 1. Up, upregulated; down, downregulated.

(E and F) Volcano plots of the differentially expressed coding genes in (E) MR766-infected and (F) Paraiba-infected hNSCs at 3 days post-infection at an MOI of 1. Blue circles represent significantly (adjusted p < 0.05) differentially expressed genes. The size of each circle is proportional to the square root of the base mean expression of the gene.

(G) Scatterplot matrix comparing the relative gene expression of 20 top differentially expressed genes in ZIKV MR766- and Paraiba-infected hNSCs under varying MOIs and time points. Plots show the correlation between differentially expressed genes in MR766-versus Paraiba-infected neural stem cells infected under 4 conditions: with MR766 at an MOI of 1 and analyzed 2 days post-infection; with Paraiba at an MOI of 1 and analyzed 2 or 4 days post-infection; or with Paraiba at an MOI of 3 and analyzed 2 days post-infection. Points represent the mean relative expression level of 20 top differentially expressed genes relative to mock-infected cells in each condition. n = 6 biological replicates.

See also Figure S1.