RNA-Seq-Based Whole Transcriptome Analysis of IPEC-J2 Cells During Swine Acute Diarrhea Syndrome Coronavirus Infection

Fanfan Zhang; Weifeng Yuan; Zhiquan Li; Yuhan Zhang; Yu Ye; Kai Li; Zhen Ding; Yunyan Chen; Ting Cheng; Qiong Wu; Yuxin Tang; Deping Song

doi:10.3389/fvets.2020.00492

RNA-Seq-Based Whole Transcriptome Analysis of IPEC-J2 Cells During Swine Acute Diarrhea Syndrome Coronavirus Infection

Front Vet Sci. 2020 Aug 13:7:492. doi: 10.3389/fvets.2020.00492. eCollection 2020.

Authors

Fanfan Zhang^{1

2

3}, Weifeng Yuan^{1

2}, Zhiquan Li^{1

2}, Yuhan Zhang^{1

2}, Yu Ye^{1

2}, Kai Li^{1

2}, Zhen Ding^{1

2}, Yunyan Chen⁴, Ting Cheng⁴, Qiong Wu^{1

2}, Yuxin Tang^{1

2}, Deping Song^{1

2}

Affiliations

¹ Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.
² Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.
³ Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, China.
⁴ College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.

Abstract

The new emergence of swine acute diarrhea syndrome coronavirus (SADS-CoV) has resulted in high mortality in suckling pigs in China. To date, the transcriptional expression of host cells during SADS-CoV infection has not been documented. In this study, by means of RNA-Seq technology, we investigated the whole genomic expression profiles of intestinal porcine epithelial cells (IPEC-J2) infected with a SADS-CoV strain SADS-CoV-CH-FJWT-2018. A total of 24,676 genes were identified: 23,677 were known genes, and 999 were novel genes. A total of 1,897 differentially expressed genes (DEGs) were identified between SADS-CoV-infected and uninfected cells at 6, 24, and 48 h post infection (hpi). Of these, 1,260 genes were upregulated and 637 downregulated. A Gene Ontology enrichment analysis revealed that DEGs in samples from 6, 24, and 48 hpi were enriched in 79, 383, and 233 GO terms, respectively, which were mainly involved in immune system process, response to stimulus, signal transduction, and cytokine-cytokine receptor interactions. The 1,897 DEGs were mapped to 109 KEGG Ontology (KO) pathways classified into four main categories. Most of the DEGs annotated in the KEGG pathways were related to the immune system, infectious viral disease, and signal transduction. The mRNA of porcine serum amyloid A-3 protein (SAA3), an acute phase response protein, was significantly upregulated during the infection. Over-expressed SAA3 in IPEC-J2 cells drastically inhibited the replication of SADS-CoV, while under-expressed SAA3 promoted virus replication. To our knowledge, this is the first report on the profiles of gene expression of IPEC-J2 cells infected by SADS-CoV by means of RNA-Seq technology. Our results indicate that SADS-CoV infection significantly modified the host cell gene expression patterns, and the host cells responded in highly specific manners, including immune response, signal and cytokine transduction, and antiviral response. The findings provide important insights into the transcriptome of IPEC-J2 in SADS-CoV infection.

Keywords: RNA-Seq; SADS-CoV; gene expression; porcine serum amyloid A-3; transcriptome.