Screening and Analysis of Differentially Expressed Genes in Vero Cells Infected with Porcine epidemic diarrhea virus
YANG Lin1, LIU Ying1, SHU Jin-Qi1, TAO Si-Rui1, JIANG Cai-Ying1,*, SHU Jian-Hong1,2,*
1 College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; 2 Shaoxing Biomedical Research Institute, Zhejiang Sci-Tech University, Shaoxing 312000, China
Abstract：Porcine epidemic diarrhea virus (PEDV) is the pathogen that causes porcine (Sus scrofa domesticus) epidemic diarrhea. PEDV infection mainly causes severe diarrhea, vomiting and dehydration in pigs, resulting in extremely high mortality of pigs. The mortality rate of piglets within 6 days of age after infection with PEDV is even as high as 100%, which has caused great economic losses to the pig industry in the world, which seriously affected the healthy development of the pig industry. In order to study the pathogenic mechanism of PEDV, PEDV was inoculated into Vero cells cultured in vitro, and total RNA from non-infected PEDV control group, PEDV 12 h group, and PEDV 24 h group Vero cells was extracted for Illumina high-throughput sequencing. 56789250, 48406834, 52574920, 51348394, 62905540, 54244594, 50051472, 67574592, and 57516788 sequencing raw data were obtained, respectively. The raw data was filtered, and 56126966, 47748166, 51932440, 50756174, 62190894, 53605948, 49571034, 66728750, and 56851386 filtered data (clean reads) were obtained. The correlation coefficients between samples were all greater than 0.98, indicating that the correlation between samples was qualified. Bioinformatics analysis of the sequenced data revealed that compared with the group uninfected with PEDV, there were 4 differentially expressed genes in the group infected with PEDV 12 h (P<0.05), and 1 498 differentially expressed genes in the group infected with PEDV for 24 h (P<0.05), respectively; compared with the group infected with PEDV for 12 h, there were 1 643 differentially expressed genes in the group infected with PEDV for 24 h (P<0.05). Five differentially expressed genes were randomly selected for qRT-PCR verification analysis, and the verification results were consistent with the transcriptome sequencing results, indicated that the transcriptome sequencing results were relatively reliable and can be used for further bioinformatics analysis. The Gene Ontology (GO) function annotation analysis was performed on the differentially expressed genes screened above. The GO annotations of differentially expressed genes were classified into three aspects of biological process, cell composition, and molecular function, respectively, and involved cell process, biological regulation, metabolic processes, cell composition, organelle composition, and catalytic activity. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed on the above-mentioned differentially expressed genes, and the results showed that when Vero cells were infected with PEDV for 12 h, 4 differentially expressed genes in the African green monkey (Chlorocebus sabaeus) genome gene annotation were enriched in the NOD-like receptor signaling pathway and microRNAs in cancer signaling pathway; For 24 h post-infection, some cells exhibited severe cytopathic effects, while most of the cells were not detached from the well bottom of culture plates, the differentially expressed genes in the African green monkey genome gene annotation were mainly concentrated in TNF (tumor necrosis factor) signal pathway, P53 (tumor protein 53) signal pathway, Jak-STAT (Janus kinase/signal transducer and activator of tran-ions) signal pathway, MAPK (mitogen-activated protein kinase) signal pathway and immune inflammation, respectively. According to the signal pathway activated by PEDV infection, it can be judged that when cells were infected with PEDV, they can affect the virus's ability to invade and replicate by regulating autoimmunity and inducing apoptosis. The differentially expressed genes found in this study provide data references for further research on the pathogenic mechanism of PEDV.
杨琳, 刘影, 舒金琪, 陶思锐, 蒋彩英, 舒建洪. 猪流行性腹泻病毒感染Vero细胞差异表达基因的筛选与分析[J]. 农业生物技术学报, 2021, 29(2): 327-339.
YANG Lin, LIU Ying, SHU Jin-Qi, TAO Si-Rui, JIANG Cai-Ying, SHU Jian-Hong. Screening and Analysis of Differentially Expressed Genes in Vero Cells Infected with Porcine epidemic diarrhea virus. 农业生物技术学报, 2021, 29(2): 327-339.
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