Transcriptome analysis reveals modulation of the STAT family in PEDV-infected IPEC-J2 cells

Abstract

Background Porcine epidemic diarrhea virus (PEDV) is a causative agent of serious viral enteric disease in suckling pigs. Such diseases cause considerable economic losses in the global swine industry. Enhancing our knowledge of PEDV-induced transcriptomic responses in host cells is imperative to understanding the molecular mechanisms involved in the immune response. Here, we analyzed the transcriptomic profile of intestinal porcine epithelial cell line J2 (IPEC-J2) after infection with a classical strain of PEDV to explore the host response. Results In total, 854 genes were significantly differentially expressed after PEDV infection, including 716 upregulated and 138 downregulated genes. Functional annotation analysis revealed that the differentially expressed genes were mainly enriched in the influenza A, TNF signaling, inflammatory response, cytokine receptor interaction, and other immune-related pathways. Next, the putative promoter regions of the 854 differentially expressed genes were examined for the presence of transcription factor binding sites using the MEME tool. As a result, 504 sequences (59.02%) were identified as possessing at least one binding site of signal transducer and activator of transcription (STAT), and five STAT transcription factors were significantly induced by PEDV infection. Furthermore, we revealed the regulatory network induced by STAT members in the process of PEDV infection. Conclusion Our transcriptomic analysis described the host genetic response to PEDV infection in detail in IPEC-J2 cells, and suggested that STAT transcription factors may serve as key regulators in the response to PEDV infection. These results further our understanding of the pathogenesis of PEDV.

Prognostic association of starvation-induced gene expression in head and neck cancer

“…After 24-h starvation, mRNA sequencing of SAS cells detected 12 up-regulated ARGs (ATP6V0A2, ATP6V1B1, ATP6V1C2, DDIT3, ERN1, NHLRC1, NUPR1, PIM2, TMEM150A, TRIB3, WIPI1, and XBP1) and 13 down-regulated ARGs (BNIP3, BNIP3L, C10orf10, DAPK2, GAPDH, HMOX1, MEFV, PLK2, RRAGD, SESN3, SRPX, S100A8, and S100A9), again supporting the induction of autophagy of SAS cells under serum starvation. These genes differed from the ARGs previously reported to predict the prognosis of HNSCC patients 29 , 33 , 34 . This starvation-induced approach may be beneficial in extrapolating ARGs that have not been previously identified as differentially expressed genes.…”

“…Similarly, Jin et al 33 determined 35 genes for HNSCC and identified ITGA3, CDKN2A, FADD, NKX2-3, BAK1, CXCR4, and HSPB8 as prognostic ARGs. Ren et al 34 also reported 13 ARGs as genes that predict prognosis. In the present study, HNSCC cells were cultured under serum starvation, which can efficiently induce autophagy, and RNA sequencing was used to examine the expression of ARGs.…”

“…The complex multi-step process of autophagy is tightly controlled by a set of autophagy-related genes (ARGs). Some ARGs have been shown to be associated with the prognosis of HNSCC patients using bioinformatics 29 , 32 – 34 . However, it has not been clarified how these ARGs exhibit their expression kinetics in an environment where autophagy occurs.…”

Genome-wide transcriptome analysis of porcine epidemic diarrhea virus virulent or avirulent strain-infected porcine small intestinal epithelial cells

“…Advancements in RNA-sequencing technologies have provided us an opportunity to understand the complex host-virus interaction in detail ( Jones et al., 2014 ; Liu et al., 2019 ). Previous studies have performed the global analysis of host transcriptomic signatures to gain insights into the host response to PEDV infection at the late stages of virus infection ( Hu et al., 2020 ; Shen et al., 2020 ). Herein, we provide, for the first time, a view of genome-wide alterations in the host transcriptome that occur in response to PEDV infection, with a focus on differences in the host response to virulent (GDS01) and avirulent (HX) PEDV strains at the early stages of infection.…”

“…The RNA-sequencing analysis of the PEDV-infected cultured pig intestinal cells revealed the perturbation of signal transducer and activator of transcription, cell cycle, and apoptosis pathways at the later stages of infection ( Shen et al., 2020 ). In a similar context, a few studies have identified several key host genes involved in regulating the antiviral immune response against PEDV such as FOSL1, IL1A, ISG15, and some other ISGs ( Hu et al., 2020 ; Sun et al., 2019 ; Wang et al., 2019 ). However, the host transcriptomic landscape at an early phase of PEDV infection and differences in the host response upon infection with an avirulent or a virulent PEDV strain are currently unknown.…”