ZIKV infection strongly induces antiviral immune responses in human NPCs

To investigate the cellular pathologies in human NPCs after ZIKV infection, we performed global transcriptome profiling of the FD, FV, and H&S organoids at 3 and 6 dpi. We found 105 upregulated genes in the FD NPCs, 60 genes in the FV NPCs, and 168 genes in the H&S NPCs, with at least 1.5-fold differences found between ZIKV-infected groups and the control groups at 6 dpi. Among them, 28 genes overlapped in all three regional NPCs. These 28 common genes exclusively referred to the pathways associated with immune responses to viral infection, which could be clustered to the ISG family. Overall design: Three regional organoids were infected with ZIKV at MOI=0.5 or mock infection, and total RNAs were extracted at 3 dpi or 6 dpi and used for global transcriptome analysis. RNA-seq libraries were generated from duplicated samples per condition using the Next Illumina Ultra RNA library prep kit (NEB) following manufacturer's protocols. RNA concentration of library was measured using Qubit RNA Assay Kit in Qubit 2.0. The insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and then accurate quantification was performed with Taqman fluorescence probe of AB Step One Plus Real-Time PCR system and sequenced by an Illumina Hiseq 2500 platform.