Effects of African swine fever virus on mRNAs and microRNAs Expression Patterns of Porcine Alveolar Macrophages

doi:10.7668/hbnxb.20193131

Abstract

Abstract:

The aim of this study was to investigate the effect of African swine fever virus(ASFV) after infecting swine alveolar macrophages in vivo. Based on the mRNAs and microRNAs sequencing data of pig alveolar macrophages(PAMs)infected with ASFV,using bioinformatics software to process the data to obtain a number of differentially expressed genes;using gene function enrichment and corresponding protein interaction to analyze biological pathways;and using mRNAs and microRNAs interaction to confirm the important target relationships. The results showed that ASFV changed the expression level of 1 181 genes in PAMs;mainly regulate the host in the energy metabolism processes(eg.,lipid decomposition,organic hydroxy compound metabolism,carbohydrate catabolism,monocarboxylic acid metabolism),and also in the cell-cycle process(eg.,mitotic cell cycle process,cell cycle phase transition,cell cycle positive regulation);ASFV also elicited the differential expression of 25 microRNAs in PAMs,including the virus-related miR-27b-3p,miR-193a-3p,and miR-132,etc.;however,miR-27b-3p,as the differential microRNA with the highest expression abundance,had a target relationship with some important differential genes(eg.,PLK2,HSP90AA1,etc.),and regulated the body's immunity and cell cycle-related pathways. In conclusion,this study showed that the mode of action after ASFV infection with PAMs included destroying the host homeostasis through energy metabolism and cell cycle,and breaking the microRNAs regulation balance of the body;and small RNAs such as miR-27b-3p could be used as target molecules for ASFV research.

Key words: Swine, ASFV, Porcine alveolar macrophages, mRNAs, microRNAs

ZHANG Tinghuan, CHAI Jie, CHEN Li, LONG Xi, GUO Zongyi. Effects of African swine fever virus on mRNAs and microRNAs Expression Patterns of Porcine Alveolar Macrophages[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(S1): 348-357. doi: 10.7668/hbnxb.20193131.

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Figures/Tables 9

Fig.1 Difference analysis of genes expression A.PCA analysis;B.Difference analysis of ASFV_24 h group and Mock_24 h group;C.Difference analysis of ASFV_24 h group and ASFV_0 h group;D.The overlaps of two sets of differential genes.

Fig.2 Changes of genes expression A-C. The expression levels of LPL, FABP4 and FABP5, respectively; D-F. The expression levels of KLF4, FosB and CCl4, respectively. The significance between different groups is indicated by capital letters. The same letter indicates that the expression amount is not significant (P>0.05), and the different letters indicate that the expression amount is very significant (P< 0.01).The same as Fig.9.

Fig.3 Functional enrichment analysis of differential genes A.ASFV_ Up genes enrichment pathways;B. ASFV_ Down gene enrichment pathways.

Fig. 4 The protein-protein interaction analysis of ASFV_Up genes A-B.The interaction networks and functional enrichment analysis of ASFV_ up genes related proteins;C-D.The interaction networks and functional enrichment analysis of MCODE1;E-F.The interaction networks and functional enrichment analysis of MCODE2.The same as Fig.5.

Fig.5 The protein-protein interaction analysis of ASFV_Down genes

Fig.6 Difference analysis of microRNAs expression A.PCA analysis;B. Difference analysis of ASFV_24 h group and ASFV_0 h group;C. Difference analysis of ASFV_24 h group and Mock_24 h group;D. The overlaps of two sets of differential micoRNAs;E. The heat map of differential microRNAs expression.

Fig.7 Expression abundance and targets prediction of differential microRNAs A. ASFV_ Up microRNAs;B. ASFV_Down microRNAs. The color of dots represent the average expression abundance of microRNAs,in which red represents RPM>10⁴,orange represents RPM>100,gray represents RPM <10 and black represents RPM<1;The size of the dots represent the number of targets. The larger the dot,the more targets;The thickness of the line between different microRNAs represents the number of shared targets. The thicker the line,the more shared targets.

Fig.8 Conservation of miR-27b-3p and Enrichment function of its targets A.Sequence conservation analysis of miR-27b-3p among different species;B-C. The overlaps of miR-27b-3p targets by miRanda and Targetscan;D. Functional enrichment analysis of miR-27b-3p targets.

Fig.9 Conservation of miR-27b-3p target sites and the expression change of targets A.The binding sites of miR-27b-3p and 3'UTR region of PLK2 gene were conserved among different species;B.Changes in the expression of PLK2 gene;C.The binding sites of miR-27b-3p and 3'UTR region of HSP90AA1 gene were conserved among different species;D.Changes in the expression of HSP90AA1 gene.

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