Fig. 3
Th1-like Tfh cells have characteristics of both Tfh and Th1 cells. IFN-γ-YFP reporter mice were administered with ZIKV with or without anti-IFNAR1 blocking antibody as described in Fig.1. Splenocytes were harvested on 7 dpi for RNA-seq analyses. a Heatmap of the significantly different expression of global genes (rows) in IFN-γ− Tfh (Tfh; replicates 1 and 2), Th1-like Tfh (Th1-like Tfh; replicates 1 and 2), and Th1 (Th1; replicates 1 and 2) cells (columns). BH-adjusted p value (FDR), α < 0.05, 1.5-fold change in Th1-like Tfh cells vs. Tfh cells, threefold change in Th1-like Tfh cells vs. Th1 cells. b Scatter plot analysis of the expression of Tfh cell (left) and Th1 cell (right)-related genes in Th1-like Tfh cells compared with IFN-γ− Tfh (adjusted p-value < 0.05, fold change > 1.5) and Th1 cells (adjusted p-value < 0.05, fold change > 3). c, d Heatmap of the significantly different expression of c Tfh-related genes (rows), d Th1-related genes (rows) in IFN-γ− Tfh (Tfh; replicates 1 and 2), Th1-like Tfh (Th1-like Tfh; replicates 1 and 2), and Th1 (Th1; replicates 1 and 2) cells (columns). FDR, α < 0.05. e Heatmap of the significantly different expression of genes (rows) in Th1-like Tfh cells (Th1-like Tfh; replicates 1 and 2) compared with IFN-γ− Tfh (Tfh; replicates 1 and 2) and Th1 (Th1; replicates 1 and 2) cells (columns). FDR, α < 0.05. f Enrichment of upregulated pathways in Th1-like Tfh cells, with the top 23 pathways listed. FDR q-value < 0.05. g Enrichment of gene signatures related to the Kyoto Encyclopedia of Genes and Genomes Negative Regulation of Viral Genome Replication (up, NES is 2.026; FDR q-value is 0.0183) and DNA Dependent DNA replication pathway (down, NES is 2.112; FDR q-value is 0.0159) in Th1-like Tfh cells. Data (a–g) are pooled from two independent technical duplicates
