Transcriptome profiles of organ tissues from pigs experimentally infected with African swine fever virus in early phase of infection

Abstract

African swine fever, caused by African swine fever virus (ASFV), is a highly contagious and fatal disease that poses a significant threat to the global pig industry. The limited information on ASFV pathogenesis and ASFV-host interactions has recently prompted numerous transcriptomic studies. However, most of these studies have focused on elucidating the transcriptome profiles of ASFV-infected porcine alveolar macrophages in vitro. Here, we analyzed dynamic transcriptional patterns in vivo in nine organ tissues (spleen, submandibular lymph node, mesenteric lymph node, inguinal lymph node, tonsils, lungs, liver, kidneys, and heart) obtained from pigs in the early stages of ASFV infection (1 and 3 d after viremia). We observed rapid spread of ASFV to the spleen after viremia, followed by broad transmission to the liver and lungs and subsequently, the submandibular and inguinal lymph nodes. Profound variations in gene expression patterns were observed across all organs and at all time-points, providing an understanding of the distinct defence strategies employed by each organ against ASFV infection. All ASFV-infected organs exhibited a collaborative response, activating immune-associated genes such as S100A8, thereby triggering a pro-inflammatory cytokine storm and interferon activation. Functional analysis suggested that ASFV exploits the PI3K-Akt signalling pathway to evade the host immune system. Overall, our findings provide leads into the mechanisms underlying pathogenesis and host immune responses in different organs during the early stages of infection, which can guide further explorations, aid the development of efficacious antiviral strategies against ASFV, and identify valuable candidate gene targets for vaccine development.

Keywords: African swine fever; differentially expressed gene; immune response; organ tissue tropism; transcriptome.

Figure 1.

ASFV DNA copies in the various organ tissues (approximately 1 g) collected from pigs in the ASFV infection group. Red bars indicate the mean value in each tested organ tissue. *p < 0.05. LN: lymph node; ASFV, African swine fever virus; dpi, days post-infection

Figure 2.

Heatmap plots representing the expression profile of DEGs involved in the different immune responses in each organ tissue from the ASFV-inoculated pigs (TRT pigs) euthanized at 1 and 3 dpi. SLN, submandibular lymph node; MLN, mesenteric lymph node; ILN, inguinal lymph node; DEGs, differentially expressed genes; ASFV, African swine fever virus

Figure 3.

Gene expression patterns of cytokines and their receptors in organ tissues (tonsils, spleen, SLN, MLN, lungs, liver, kidneys, ILN, and heart) from ASFV-inoculated pigs (TRT) euthanized at 3 dpi. (A) ILs and their receptors. (B) IFNs. (C) Genes of the TNF-receptor superfamily. (D) Chemokines and their receptors. SLN, submandibular lymph node; MLN, mesenteric lymph node; ILN, inguinal lymph node; TNF, tumour necrosis factor; ASFV, African swine fever virus; IFN, interferon; IL, interleukin

Figure 4.

Illustration of the conserved immune-related pathways in organ tissues (the spleen, SLN, MLN, ILN, tonsils, lungs, liver, kidneys, and heart) from ASFV-inoculated pigs (TRT) euthanized at (A) 1 and (B) 3 dpi. The KEGG pathways terms are listed on the left, and p-value and gene counts are shown on the right. SLN, submandibular lymph node; MLN, mesenteric lymph node; ILN, inguinal lymph node; KEGG, Kyoto Encyclopedia and Gene and Genomes; ASFV, African swine fever virus; IL, interleukin; PI3 K, phosphoinositide 3-kinase; NF-κB, nuclear factor-kappa B; dpi, days post-inoculation

Figure 5.

(A) PPI network for the 75 common DEGs identified in the nine organ tissues (spleen, submandibular lymph node, mesenteric lymph node, inguinal lymph node, tonsils, lungs, liver, kidneys, and heart) from ASFV-inoculated pigs (TRT pigs) euthanized at 3 dpi. A total 164 nodes and 2,444 interaction associations were detected. (B) Module analysis from the PPI network. The Top 3 significant modules (Module 1, 2, and 3) were obtained from the PPI network of DEGs, using MCODE. PPI, protein-protein interaction; ASFV, African swine fever virus; DEGs, differentially expressed genes; dpi, days post-inoculation.