Differential expression and correlation analysis of miRNA–mRNA profiles in swine testicular cells infected with porcine epidemic diarrhea virus

Abstract

The variant virulent porcine epidemic diarrhea virus (PEDV) strain (YN15) can cause severe porcine epidemic diarrhea (PED); however, the attenuated vaccine-like PEDV strain (YN144) can induce immunity in piglets. To investigate the differences in pathogenesis and epigenetic mechanisms between the two strains, differential expression and correlation analyses of the microRNA (miRNA) and mRNA in swine testicular (ST) cells infected with YN15, YN144, and mock were performed on three comparison groups (YN15 vs Control, YN144 vs Control, and YN15 vs YN144). The mRNA and miRNA expression profiles were obtained using next-generation sequencing (NGS), and the differentially expressed (DE) (p-value < 0.05) mRNA and miRNA were obtained using DESeq R package. mRNAs targeted by DE miRNAs were predicted using the miRanda algortithm. 8039, 8631 and 3310 DE mRNAs, and 36, 36, and 22 DE miRNAs were identified in the three comparison groups, respectively. 14,140, 15,367 and 3771 DE miRNA–mRNA (targeted by DE miRNAs) interaction pairs with negatively correlated expression patterns were identified, and interaction networks were constructed using Cytoscape. Six DE miRNAs and six DE mRNAs were randomly selected to verify the sequencing data by real-time relative quantitative reverse transcription polymerase chain reaction (qRT-PCR). Based on bioinformatics analysis, we discovered the differences were mostly involved in host immune responses and viral pathogenicity, including NF-κB signaling pathway and bacterial invasion of epithelial cells, etc. This is the first comprehensive comparison of DE miRNA–mRNA pairs in YN15 and YN144 infection in vitro, which could provide novel strategies for the prevention and control of PED.

Integrated miRNA and mRNA Expression Profiles Reveal Differentially Expressed miR-222a as an Antiviral Factor Against Duck Hepatitis A Virus Type 1 Infection

“…Similarly, several studies were also mapped to precursor/mature miRNAs of chicken or other animals in miRbase to annotate conserved miRNAs ( Cui et al., 2018 ; Wu et al., 2018 ; Wu et al., 2019a ; Yang et al., 2020 ). In addition, miRNA length showed that the majority had a length of 23 nt and the first nucleotide base revealed U predominance in the identified miRNAs ( Figure 2 ), which is consistent with the findings of other studies ( Chen et al., 2021 ; Zhang et al., 2021 ).…”

Characteristics of the MicroRNA Expression Profile of Exosomes Released by Vero Cells Infected with Porcine Epidemic Diarrhea Virus

“…PEDV is a coronavirus that causes acute and highly contagious intestinal infectious diseases in piglets [28]. PEDV infection leads to dynamic changes of miRNA expression in the host cells and forms a complex interaction network with the virus [29,30]. In recent years, the use of high-throughput sequencing techniques to reveal the integration of miRNAs and mRNAs in viral infection has proven to be helpful in elucidating the regulatory mechanism of miRNA.…”

Differential MicroRNA Expression in Porcine Endometrium Related to Spontaneous Embryo Loss during Early Pregnancy

“…In addition, downregulating Forkhead box other 1 ( FOXO1 ) expression eventually leads to decidua damage [ 28 ]. The Rap1 signaling pathway is a crucial immune-related pathway and cancer-related pathway [ 29 , 30 ]. The expression of cell adhesion molecules is critical for embryo implantation and pregnancy establishment [ 31 ].…”