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

Figures & data

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

Table 1. List of overlapping DEGs in the nine organ tissues obtained from ASFV-infected pigs euthanized at 1 and 3 dpi.

Group	Tissues	No. of genes	Overlapping DEGs
3 dpi	Spleen, SLN, MLN, ILN, tonsils, lungs, liver, kidneys, heart	74	PRORP, DNAJB4, PPIDEIF4E, CYSLTR1, FCF1, BLZF1, DCHS1, NDUFA5, PSMA1, CHMP5, COL6A2, UBD, HSPH1, TSPAN6, PPA1, BIRC3, CAM, PPL, MIX23, FRS3, COL4A2, ENSSSCG00000031170, PLSCR1, HSPE1, RPS27L, SREBF1, AUTS2, PPARGC1B, KCP, TOM1L2, IFIT2, CDC42BPG, HR, GLI3, CLIC2, FUNDC1, FLRT1, DPY30, CHORDC1, TMEM156, UVSSA, CELSR2, LTBP3, ARL5B, KIAA1143, PRDX1, RBX1, MFSD1, PSMA2, RPL26, NT5C3A, FI44L, XD3, C21orf91, COL6A1, UBE2V2, COL5A1, CCT8, TMEM33, GABBR1, LSM3, ORMDL1, SNRPG, SOGA1, GPX8, DENND2B, HIST1, H2BD, SOX18, APLNR, DNAJA1, KBTBD11, IFIT5
1 dpi	Spleen, SLN, MLN, ILN, tonsils, lungs, liver, kidneys, heart	8	S100A8, IDO1, S100A12, ZSWIM9, CXCL10, TFEC, FRS3, SH2D1A, ARL5B, CXCL9

dpi, days post-inoculation; SLN, submandibular lymph node; MLN, mesenteric lymph node; ILN, inguinal lymph node; ASFV, African swine fever virus; DEGs, differentially expressed genes

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

Table 2. List of overlapping immune-associated pathways that were significantly (p < 0.05) enriched with DEGs identified in organ tissues from ASFV-infected pigs, at 1 and 3 dpi

Group	Overlapping immune-related pathways	Tissues	Top overlapping genes
1 dpi	PI3K-Akt signalling pathway	Heart, ILN, kidney, liver, lung, MLN, muscle, spleen, SLN, tonsils	COL4A2, COL6A2, COL6A1, NGFR, COL9A3
	IL-17 signalling pathway	ILN, kidneys, liver, MLN, tonsils, spleen	S100A8, IL5, CXCL10, LCN2, HSP90AA1
	Viral protein interaction with cytokine and cytokine receptor	Kidneys, lungs	CCR10, CXCL9, CXCL10, CCR1, IL22RA1
	Primary immunodeficiency	Heart, kidneys, SLN	ICOS, CD8A, LCK, CD3E, PTPRC
	T cell receptor signalling pathway	Heart, kidneys, MLN	ICOS, ITK, CD3E, MAPK11, IL5
	Viral carcinogenesis	MLN, muscle, SLN	IL6ST, HPN, PRKACB, SNW1, NRAS
	Complement and coagulation cascades	Heart, ILN, kidneys, lungs, tonsils	C6, C7, FGB, TFPI, CFI
	TGF-β signalling pathway	MLN, SLN, tonsils	INHBA, SP1, DCN, PPP2R1B, SMURF2
	Cytokine-cytokine receptor interaction	Heart, ILN, kidneys, lungs	CXCL9, CXCL10, IL33, ACVR1C, BMP10
3 dpi	PI3K-Akt signalling pathway	Heart, ILN, kidneys, liver, lungs, MLN, muscle, spleen, SLN, tonsils	COL4A2, COL6A2, COL4A1, LAMA5, COL1A1
	NF-κB signalling pathway	Heart, ILN, kidneys, liver, lungs, MLN, muscle, spleen, SLN, tonsils	CD40, VCAM1, CCL4, IRAK4, IL1R1
	Chemokine signalling pathway	Heart, kidneys, liver, lungs, MLN, muscle, SLN, tonsils, spleen	CXCL11, CXCL9, CXCL10, CCL2, CCL19
	IL-17 signalling pathway	Heart, ILN, kidneys, liver, lungs, MLN, tonsils, spleen	CXCL10, CCL2, MAPK7, CXCL8, HSP90B1
	Complement and coagulation cascades	Heart, kidneys, liver, lungs, SLN, tonsils, spleen	C1QB, C5, C7, C1QA, C1QC
	Toll-like receptor signalling pathway	Heart, ILN, kidneys, spleen	CXCL10, LY96, CXCL9, CXCL11, CCL4
	T cell receptor signalling pathway	Heart, ILN, muscle, spleen	NRAS, CD3E, JUN, ITK, PPP3CA
	Cytokine-cytokine receptor interaction	Heart, kidneys, liver, spleen	CXCL10, CCL2, CXCL11, CXCL9, IL17B
	TGF-β signalling pathway	Heart, lungs, SLN, tonsils	TGFBR1, PPP2R1B, NOG, RBX1, ZFYVE16
	Viral protein interaction with cytokine and cytokine receptor	Heart, liver, spleen	CXCL8, CXCL10, CXCL9, CCL2, CXCL11

SLN, submandibular lymph node; MLN, mesenteric lymph node; ILN, inguinal lymph node; NF-κB, nuclear factor-kappa B; TGF-β, transforming growth factor-beta; PI3 K, phosphoinositide 3-kinase; 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.

Data availability statement

The transcriptomic datasets generated in this study can be found in the NCBI GEO database, under accession number 230340.