Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Compare of differential expression profiles of PEDV-susceptible and non-susceptible cell lines at the transcriptome level to identify key molecules associated with PEDV entry

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE236338 | GEO | 2023/07/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identification of cell types and transcriptome landscapes of PEDV infected porcine small intestine using single-cell RNA-sequencing

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

comparative proteome analysis of serum exosomes from newborn piglets inresponse to porcine epidemic diarrhea virus infection

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

Comparative gene expression analysis between virus-susceptible and -resistant rice lines (NIL37 and NIL22)

2007-10-25 | GSE6126 | GEO

Comparative gene expression analysis between virus-susceptible and -resistant rice lines (TW16-1263 and -1029)

Project description:Near-isogenic lines TW16-1263 and TW16-1029 were developed from the cross between TN1 (recurrent parent susceptible to rice tungro spherical virus (RTSV)) and Utri Merah (donor parent resistant to RTSV). TW16-1263 is susceptible to RTSV, whereas TW16-1029 is resistant to RTSV. In order to identify genes which are constitutively differentially expressed between TW16-1263 and TW16-1029, the gene expression in the two lines were compared at three different conditions (healthy, green leafhopper (GLH)-inoculated, and RTSV-inoculated). Keywords: Constitutive differential expression

2007-10-25 | GSE6125 | GEO

Comparative gene expression analysis between virus-susceptible and -resistant rice lines (TW16-4 and -69)

Project description:Near-isogenic lines TW16-4 and TW16-69 were developed from the cross between TN1 (recurrent parent susceptible to rice tungro spherical virus (RTSV)) and Utri Merah (donor parent resistant to RTSV). TW16-4 is susceptible to RTSV, whereas TW16-69 is resistant to RTSV. In order to identify genes which are constitutively differentially expressed between TW16-4 and TW16-69, the gene expression in the two lines were compared at three different conditions (healthy, green leafhopper (GLH)-inoculated, and RTSV-inoculated). Keywords: Constitutive differential expression

2007-10-25 | GSE6124 | GEO

Transcription profiling of rice virus-susceptible and -resistant lines NIL37 and NIL22

Project description:Near-isogenic lines NIL37 and NIL22 were developed from the cross between Ilpum (recurrent parent susceptible to rice stripe virus (RSV)) and Shinkwang (donor parent resistant to RSV). NIL37 is susceptible to RSV, whereas NIL22 is resistant to RSV. In order to identify genes which are constitutively differentially expressed between NIL37 and NIL22, the gene expression in the two lines were compared at two different conditions (healthy, and RSV-inoculated). Experiment Overall Design: Total RNA was isolated from 14-day old plants of NIL37 and NIL22 at two different conditions (healthy and RSV-inoculated). The levels of gene expression in the two lines of the same condition were compared by microarray. Each experiment was repeated twice.

2008-06-14 | E-GEOD-6126 | biostudies-arrayexpress

Identification of host proteins interacting with the E protein of porcine epidemic diarrhea virus

Project description:Porcine epidemic diarrhea (PED) is an acute, highly contagious, and high-mortality enterophilic infectious disease caused by the porcine epidemic diarrhea virus (PEDV). PEDV is globally endemic and causes substantial economic losses in the swine industry. The PEDV E protein is the smallest structural protein with high expression levels that interacts with the M protein and participates in virus assembly. However, how the host proteins interact with E proteins in PEDV replication remains unknown. We identified host proteins that interact with the PEDV E protein using a combination of PEDV E protein-labeled antibody co-immunoprecipitation and tandem liquid-chromatography mass-spectroscopy (LC-MS/MS).

2024-03-05 | PXD050352 | Pride

Single cell RNA-seq of spleens of chickens from Marek's-disease-resistant and -susceptible lines infected with Marek's disease virus

Project description:We infected chickens from two genetic lines, one bred to be resistant to Marek's disease and one bred to be susceptible, with the Marek's disease virus. We performed single-cell RNA sequencing of the spleens of these chickens along with age-matched uninfected controls from both lines.

2022-09-16 | E-MTAB-12145 | biostudies-arrayexpress

Wolbachia strains differ in arbovirus inhibition mechanisms in Aedes mosquitoes

Project description:Some strains of the inherited bacterium Wolbachia have been shown to be effective at reducing the transmission of dengue and other positive-sense RNA viruses by Aedes aegypti in both laboratory and field settings and are being deployed for dengue control. The degree of virus inhibition varies between Wolbachia strains; density and tissue tropism can contribute to these differences but there are also indications that this is not the only factor involved: for example, strains wAu and wAlbA are maintained at similar densities but only wAu produces strong dengue inhibition. We previously reported perturbations in lipid transport dynamics, including sequestration of cholesterol in lipid droplets, with strains wMel / wMelPop in Ae. aegypti. Here we show that strain wAu does not produce the same cholesterol sequestration phenotype despite displaying strong virus inhibition and moreover, in contrast to wMel, wAu antiviral activity was not rescued by cyclodextrin treatment. To further investigate the cellular basis underlying these differences, proteomic analysis of midguts was carried out on Ae. aegypti lines and revealed that wAu-carrying midguts showed a distinct proteome when compared to Wolbachia-free, wMel- or wAlbA-carrying midguts, in particular with respect to lipid transport and metabolism. The data suggest a possible role for perturbed RNA processing pathways in wAu virus inhibition. Together these results indicate that wAu shows unique features in its inhibition of arboviruses compared to previously characterized Wolbachia strains

2023-06-07 | MSV000092124 | MassIVE

Coronavirus replication is controlled by both host and viral RNA m6A methylations

Project description:N6–methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, and it plays an important role in RNA metabolism and function. Recent studies have revealed that viral RNA m6A modification can play an anti-viral or pro-viral role in virus life cycle. However, whether m6A methylation can modulate replication of coronaviruses, which contain the largest known RNA genomes, remains elusive. Here, we determined that m6A modifications of porcine epidemic diarrhea coronavirus (PEDV) are exclusively located in the N gene at the 3’-end of genome, and that PEDV infection alters the expression pattern of host proteins involved in m6A modification. Depletion of m6A demethylases significantly increased PEDV replication and gene expression whereas knockdown of m6A methyltransferases slightly decreased PEDV infection. Interestingly, m6A binding proteins YTHDF 2 and 3 significantly inhibited PEDV replication whereas YTHDF1 has an opposite effect. When the major m6A sites in the N gene were mutated, the resultant recombinant PEDVs and PEDV replicons had a significant increase in replication and gene expression. This study illustrates that (i) addition of m6A to PEDV RNA inhibits viral replication, and (ii) both host and viral m6A machinery regulates coronavirus replication.

2022-12-01 | GSE141291 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data