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. 2021 Sep 20;10:e69951. doi: 10.7554/eLife.69951

Figure 4. Trained innate immunity mediates vaccination-induced rapid protection.

(A) Survival of WT and Rag1-/- mice immunized intranasally (i.n.) with inactivated whole cell (IWC) (LAC-4) or PBS, challenged intratracheally (i.t.) by lethal LAC-4 7 days later (n = 5 for WT mice, n = 10 for Rag1-/- mice). **p<0.01 compared to control calculated by log-rank test. Data are representative of two independent experiments. (B–E) Rag1-/- mice were immunized with IWC (LAC-4) or PBS as control for 7 days and challenged with LAC-4. The lung tissue was collected to perform RNA-seq. (B) MA plot of the differentially expressed genes (DEGs) of IWC (LAC-4)-immunized lung (n = 3) vs. control lung of Rag1-/- mice (n = 3) at 24 hr post LAC-4 challenge. X-axis represents average counts per million (logCPM) and Y-axis represents log fold changes (logFC) in IWC-immunized mice vs. control mice. The blue line is the threshold, logFC >1 means upregulation and logFC < –1 means downregulation. (C) Top 10 Gene Ontology (GO) enrichment terms of downregulated DEGs in the IWC-immunized group at 24 hr post infection (hpi). (D) Heatmap of DEGs related to inflammatory response is shown. False discovery rate (FDR) < 0.05. (E) Reads per kilobase per million reads (RPKM) of inflammatory and chemokine genes. Data are mean ± SD. *p<0.05, **p<0.01 determined by two-tailed unpaired t test. (F) The heatmap of innate immune response-related genes (GO_0045087) of lung samples from control (n = 3), IWC (LAC-4)-immunized at day 2 (IWC-2d) (n = 2), and day 7 (IWC-7d) (n = 2) in Rag1-/- mice.

Figure 4—source data 1. Raw data for Figure 4A,E.
Figure 4—source data 2. RNA-seq results of reads per kilobase per million reads (RPKM) for all samples and all genes.

Figure 4.

Figure 4—figure supplement 1. Supplementary RNA-seq results.

Figure 4—figure supplement 1.

(A–C) RNA-seq data related to Figure 4B. (A) The heatmap of 2401 differentially expressed genes (DEGs) in lungs. (B) Numbers of upregulated and downregulated DEGs. (C) Top 10 Gene Ontology (GO) terms of upregulated DEGs. (D) Heatmap of DEGs related to inflammatory response (GO0006954). (E) Lung samples from control, inactivated whole cell (IWC)-immunized Rag1-/- mice at day 2 (IWC-2d), day 7 (IWC-7d), and IWC-immunized mice (7 day) at 24 hr after challenge with A. baumannii (IWC-7d+infection) and control mice at 24 hr after challenge (infection) were processed for RNA-seq. MA plot of DEGs in each treatment group compared with that in control group.