Ontology highlight
ABSTRACT:
PROVIDER: PRJNA730044 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14552500.fastq.gz | Fastqsanger.gz | |||
| SRR14552501.fastq.gz | Fastqsanger.gz | |||
| SRR14552502.fastq.gz | Fastqsanger.gz | |||
| SRR14552503.fastq.gz | Fastqsanger.gz | |||
| SRR14552504.fastq.gz | Fastqsanger.gz |
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Project description:Swine coronavirus-porcine epidemic diarrhea virus (PEDV) with specific susceptibility to pigs has existed for decades, and recurrent epidemics caused by mutant strains have swept the world again since 2010. Here, single-cell RNA-sequencing was used to perform a systematic analysis of pig small intestines infected with PEDV for the first time. Multiple cell types were identified by representative markers, including the unique marker DNAH11 of tuft cells. Meanwhile, the goblet and tuft cells were also susceptible to PEDV except enterocytes. PEDV infection obviously upregulated REG3G, which significantly inhibited virus replication. Notably, IFN-DELTAs in goblet and enterocyte progenitor cells were increased in virus infected piglet, and IFN-DELTA5 could induce GBP1, ISG15, OAS2 and IFITM1 dramatically raised in IPEC-J2 cells and restricted PEDV replication. Complement molecules were mainly expressed in intestinal cells excepting tuft cells, but PEDV decreased C3, C4A, and C5 in enterocytes, thus escaping the antiviral effect of C3. Finally, enterocytes expressed almost all coronavirus entry factors, and PEDV infection caused significant upregulation of the coronavirus receptor ACE2 in porcine enterocyte cells. In summary, this study systematically studied the response of different cell types in small intestine of pigs after PEDV infection, which deepened the understanding of viral pathogenesis.
2022-04-27 | GSE175411 | GEO
Project description:Transcriptome sequencing of IPEC-J2 cells infected with PEDV
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Project description:The immune system is thought to be fragile in the neonate, which is susceptible to pathogens. Exosomes are a type of vehicles existing in the body fluid and participate in many biological processes, especially the immune response. Inorder to investigate the roles that exosomes may play during virus infection in the neonate, porcine epidemic diarrhea virus (PEDV), a devastating enteric virus to newborn piglets, was selected for infection. Serum exosomes were then isolated from the newborn-piglets infected or mock-infected with PEDV and followed by a label-free LC-MS/MS based comparative quantitative proteomic analysis. Among 441 proteins detected in the serum exosomes, there were lots of complement proteins. The expression level of the complement C3, C6 and CFB suffered drastic changes due to PEDV infection. After the confirmation by western-blot assay, we then investigated the function of these exosomes on PEDV infection and discovered that the exosomes from mock-infected newborn piglets restricted PEDV infection but this inhibition disappeared after exosomes were heat-inactivated, suggesting that the complement is one of the key antiviral molecules. These findings will facilitate the understanding of the antiviral response of the neonate mediated by exosomes
2019-04-30 | PXD010762 | Pride
Project description:Porcine epidemic diarrhea virus (PEDV) is a deadly coronavirus for neonatal piglets and no effective vaccines are available. Transcriptional regulatory sequences (TRSs) are critical in regulating coronavirus discontinuous transcription. Also, TRSs contribute to a high recombination rate of coronaviruses, leading to difficulty in developing safe live vaccines. We hypothesize that recoding the TRS core sequences (TRS-CS) of PEDV can make the recombination impossible between the engineered vaccine virus and field strains or wildtype viruses. We used an infectious clone-derived reporter PEDV, dORF3-EGFP, as the backbone to generate a remodeled TRS (RMT) mutant that carries the recoded leader and body TRS-CSs. The RMT and dORF3-EGFP showed comparable replication efficiency in Vero cells. However, the incompatibility between the rewired and wildtype TRS-CSs led to few EGFP in RMT-infected cells. Furthermore, RMT and dORF3-EGFP had a similar attenuated phenotype, replication efficiency, and protective immunogenicity in neonatal pigs. RNA sequencing analysis indicated that EGFP transcription directed by the heterogenous TRS-CSs was significantly reduced to an extremely low level. Meanwhile, recombinant viruses were not detected in Vero cells and in pigs that were co-infected with RMT and a PEDV S-INDEL strain, Iowa106. In vitro and in vivo passaging of the RMT did not result in reversion mutations in the rewired TRS-CSs, introduced gaps, and disrupted wildtype TRSs. In summary, the RMT mutant was resistant to recombination and genetically stable and can be further optimized (e.g., deletion of the EGFP) to serve as a platform to develop safe PEDV live attenuated vaccines.
2023-11-04 | GSE246991 | GEO
Project description:Porcine epidemic diarrhea virus (PEDV) is a highly contagious virus that poses a serious threat to the global pig industry. Despite extensive research efforts, the functional receptor for PEDV remains unclear. In this study, we identified susceptible and non-susceptible cell lines to PEDV infection, and performed RNA-seq analysis on these cell lines. Using Weighted Gene Co-expression Network Analysis (WGCNA), we have identified the key pathways that correlated with the PEDV entry pathway. We found that cholesterol, sterols, and lipid transport and homeostasis were strongly correlated with PEDV entry, suggesting a potential role for cholesterol in PEDV entry. We then treated susceptible cell lines with a cholesterol transport inhibitor and found that inhibition of cholesterol transport could significantly inhibit PEDV entry in these cells. Together, our results suggest that cholesterol transport may play a critical role in the entry of PEDV into susceptible cells, and that targeting cholesterol transport may represent a potential strategy for controlling PEDV transmission. Our findings provide new insights into the mechanism of PEDV entry and may pave the way for the development of new therapeutic strategies against this economically important virus. Further studies are warranted to elucidate the detailed mechanism of PEDV entry, and to explore the potential of cholesterol transport inhibitors as a means of controlling PEDV transmission.
2023-07-06 | GSE236338 | GEO
Project description:Deoxynivalenol (DON) frequently detected in a wide range of foods and feeds, inducing cytotoxicity to animals and humans. N6-methyladenosine (m6A) is an important epitranscriptomic marker with high abundance in eukaryotic mammals mRNAs. However, the role of the m6A methylomes in DON damage is still poorly understood. Here, we investigated the m6A transcriptome-wide profile in intestinal porcine epithelial cells (IPEC-J2) with and without 1000 ng/mL DON treatment via m6A sequencing and RNA sequencing. In total, 5406 new m6A peaks appeared with the disappearance of 2615 peaks in DON-induced IPEC-J2. The unique m6A-modified genes in DON-induced IPEC-J2 were associated with TNF signaling pathway. We identified 733 differentially expressed mRNA transcripts with hyper-methylated or hypo-methylated m6A peaks between DON-induced IPEC-J2 and normal IPEC-J2. Protein interaction network analysis and qPCR validation suggested that CSF2 probably acts as a promising new target for combating DON damage in IPEC-J2. Our first report of m6A transcriptome-wide map of IPEC-J2 cells presented here provides a starting roadmap for uncovering m6A functions that may affect DON infection.
2020-08-13 | GSE156078 | GEO
Project description:Porcine epidemic diarrhea virus (PEDV) has reemerged as the main pathogen of piglets due to its high mutation feature. Monolaurin (ML) is a natural compound with a wide range of antibacterial and antiviral activities. However, the role of ML in PEDV infection is still unknown. This study aimed to evaluate the effect of ML on the growth performance, intestinal function, virus replication and cytokine response in piglets infected with PEDV, and to reveal the mechanism through proteomics analysis. Piglets were orally administrated with ML at a dose of 100 mg/kg·BW for 7 days before PEDV infection. Results showed that although there was no significant effect on the growth performance of piglets, ML administration alleviated the diarrhea caused by PEDV infection. ML administration promoted the recovery of intestinal villi, thereby improving intestinal function. Meanwhile, PEDV replication was significantly inhibited, and PEDV-induced expression of IL-6 and IL-8 were decreased with ML administration. Proteomics analyses showed that 38 proteins were differentially expressed between PEDV and ML+PEDV groups, and were significantly enriched in the interferon-related pathways. This suggests ML could promote the restoration of homeostasis by regulating the interferon pathway. Overall, the present study demonstrated ML could confer a protective effect against PEDV infection in piglets, and may be developed as a drug or feed additive to prevent and control PEDV disease.
2022-02-16 | PXD029561 | Pride
Project description:Two rounds of TMT relative quantitative proteomics were performed to detect cellular factors involved in p-eIF4E regulation of the synthesis of viral proteins.our first round of screening identified differentially expressed proteins in PEDV-infected cells and mock-infected cells; the cellular pathways involved were mainly the estrogen, cAMP, and calcium signaling pathways. Second round screening identified differentially expressed proteins in the PEDV-infected S209A-Vero cells vs. the PEDV-infected WT-Vero cells; the regulated cellular pathways were found to be mainly in the PI3K-Akt, focal adhesion, and mTOR signaling pathways, and the biological processes and molecular functions in which p-eIF4E played a role were related mainly to metabolism and biogenesis, catalytic activity, and stimuli response.4006 host factors were detected, of which 193 (in brown) were significantly upregulated (ratio ≥1.2, P＜0.05) and 191 (in green) were down-regulated upon PEDV infection (ratio ≤0.83, P＜0.05). 29 of the 191 down-regulated proteins were susceptible to a low level of p-eIF4E . Notably, among the 193 upregulated cellular proteins, 77 were upregulated in the WT-Vero over the S209A-Vero cells , suggesting that the WT-Vero cells are more susceptible to a high level of p-eIF4E.
2023-03-10 | PXD033916 | Pride