HSP90AB1 is a host factor that promotes porcine deltacoronavirus replication

RAB4B and Japanese encephalitis virus E protein interaction is essential for viral entry in early endosomes

RAB4B (Ras-Related GTP-Binding Protein 4b) is essential for intracellular trafficking and endosomal recycling processes. Our previous study, we demonstrated that RAB4B promotes Japanese encephalitis virus (JEV) replication in PK15 cells. However, the exact mechanisms underlying the role of RAB4B in JEV internalization remain unclear. Here, a genome-wide CRISPR/Cas9 library screen was performed, which identified RAB4B, along with other significant hits like ST8SIA4 and ELAVL1, as essential mediators of JEV replication. In vitro validation using RAB4B knockout in U251 and BV2 cells showed a significant reduction in JEV genome copies and viral titers, which were restored upon reintroducing RAB4B, confirming its pivotal role in viral propagation. Further mechanistic investigation revealed that RAB4B is required for JEV internalization into early endosomes. Co-immunoprecipitation and in vitro binding assays demonstrated a direct interaction between RAB4B and the JEV E protein, highlighting the functional importance of this interaction. In vivo experiments with RAB4B knockout mice showed a reduction in viral load in the brain and improved survival rates compared to wild-type mice. Taken together, these findings provide compelling evidence that RAB4B is indispensable for JEV entry and replication.

Association between hyperlipidemia and nephrolithiasis: A comprehensive bioinformatics analysis deciphering the potential common denominator pathogenesis

OBJECTIVE

Evidence suggests that nephrolithiasis and hyperlipidemia are linked. The study is designed to identify diagnostic biomarkers for nephrolithiasis in conjunction with hyperlipidemia using bioinformatics analysis, while exploring the potential common denominator pathogenesis.

METHODS

The NCBI Gene Expression Omnibus (GEO) database provided separate datasets for nephrolithiasis and hyperlipidemia. We employed the R limma package to detect differentially expressed genes (DEGs), which were subsequently analyzed for enrichment using Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Immune cell infiltration was analyzed by the CIBERSORT method. The WGCNA-R package clustered genes with similar expression profiles, followed by an analysis of the associations between the modules and specific traits or phenotypes. The STRING database was utilized to establish a protein-protein interaction (PPI) network and key functional modules, which were then analyzed using Cytoscape software. Diagnostic genes for both diseases were screened from core hub genes using least absolute shrinkage and selection operator (Lasso) regression. Subsequently, we generated receiver operating characteristic (ROC) curves to validate the predictive ability of these diagnostic genes for diagnosing nephrolithiasis in combination with hyperlipidemia. Lastly, the Network Analyst platform facilitated the construction of transcription factor-gene (TF-gene) and TF-miRNA regulatory networks.

RESULTS

Based on datasets of nephrolithiasis and hyperlipidemia, we identified 167 DEGs and 74 hub genes through WGCNA. Using PPI networks and machine learning techniques, we recognized three frequently diagnostic genes (HSP90AB1, HSPA5, and STUB1), which demonstrated high diagnostic validity. The functional enrichment of these three diagnostic genes primarily involved pathways related to cellular metabolism.

CONCLUSIONS

Our study identified three candidate diagnostic genes that can predict nephrolithiasis in conjunction with hyperlipidemia, providing a solid foundation for further exploration into the pathogenesis of nephrolithiasis and hyperlipidemia.

Genome-wide CRISPR/Cas9 library screen identifies C16orf62 as a host dependency factor for porcine deltacoronavirus infection

Porcine deltacoronavirus (PDCoV) is an emerging pathogen that can cause severe diarrhoea and high mortality in suckling piglets. Moreover, evidence of PDCoV infection in humans has raised concerns regarding potential public health risks. To identify potential therapeutic targets for PDCoV, we performed a genome-wide CRISPR/Cas9 library screening to find key host factors important to PDCoV infection. Several host genes in this screen were enriched, including ANPEP, which encodes the PDCoV receptor aminopeptidase N (APN). Furthermore, we discovered C16orf62, also known as the VPS35 endosomal protein sorting factor like (VPS35L), as an important host factor required for PDCoV infection. C16orf62 is an important component of the multiprotein retriever complex involved in protein recycling in the endosomal compartment and its gene knockout led to a remarkable decrease in the binding and internalization of PDCoV into host cells. While we did not find evidence for direct interaction between C16orf62 and the viral s (spike) protein, C16orf62 gene knockout was shown to downregulate APN expression at the cell surface. This study marks the first instance of a genome-wide CRISPR/Cas9-based screen tailored for PDCoV, revealing C16orf62 as a host factor required for PDCoV replication. These insights may provide promising avenues for the development of antiviral drugs against PDCoV infection.

Identification of host factors for livestock and poultry viruses: genome-wide screening technology based on the CRISPR system

Genome-wide CRISPR library screening technology is a gene function research tool developed based on the CRISPR/Cas9 gene-editing system. The clustered regularly interspaced short palindromic repeats/CRISPR-associated genes (CRISPR/Cas) system, considered the third generation of gene editing after zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN), is widely used for screening various viral host factors. CRISPR libraries are classified into three main categories based on the different functions of Cas9 enzymes: CRISPR knockout (CRISPR KO) library screening, CRISPR transcriptional activation (CRISPRa) library screening, and CRISPR transcriptional interference (CRISPRi) library screening. Recently, genome-wide CRISPR library screening technology has been used to identify host factors that interact with viruses at various stages, including adsorption, endocytosis, and replication. By specifically modulating the expression of these host factors, it becomes possible to cultivate disease-resistant varieties, establish disease models, and design and develop vaccines, among other applications. This review provides an overview of the development and technical processes of genome-wide CRISPR library screening, as well as its applications in identifying viral host factors in livestock and poultry.

A review of virus host factor discovery using CRISPR screening

The emergence of genome-scale forward genetic screening techniques, such as Haploid Genetic screen and clustered regularly interspaced short palindromic repeats (CRISPR) knockout screen has opened new horizons in our understanding of virus infection biology. CRISPR screening has become a popular tool for the discovery of novel host factors for several viruses due to its specificity and efficiency in genome editing. Here, we review how CRISPR screening has revolutionized our understanding of virus-host interactions from scientific and technological viewpoints. A summary of the published screens conducted thus far to uncover virus host factors is presented, highlighting their experimental design and significant findings. We will outline relevant methods for customizing the CRISPR screening process to answer more specific hypotheses and compile a glossary of conducted CRISPR screens to show their design aspects. Furthermore, using flaviviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as examples, we hope to offer a broad-based perspective on the capabilities of CRISPR screening to serve as a reference point to guide future unbiased discovery of virus host factors.

Host restriction factor Rab11a limits Porcine deltacoronavirus invasion of cells via fusion peptide-mediated membrane fusion

Porcine deltacoronavirus (PDCoV) poses a serious threat to pork industry and has the potential for cross-species transmission. Yet, the invasion mechanisms and host factors involved are still unknown. In the present work, using siRNA interference and co-immunoprecipitation, we identified Annexin A2 (ANXA2), Prohibitin-2 (PHB2), or Caveolin-2 (CAV2) as host factors positively regulating the internalization of PDCoV. We further found that Rab11a co-localized with PDCoV S and inhibited PDCoV internalization. Subsequently, a pseudoviral infection model (LV-PDCoV S-GFP) was constructed, and ANXA2 or CAV2 promoted PDCoV invasion by downregulating Rab11a. Our results also indicated that ANXA2, CAV2, and Rab11a interact with the S protein via S-FP, thereby regulating virus-host membrane fusion. Through LV-PDCoV S-GFP infection, we found that Rab11a may act as a host restriction factor, and it could regulate the invasion efficiency of PDCoV by adding of exogenous GTP. These findings revealed that Rab11a was an exciting target to restrict fusion of PDCoV with host cell membranes. AVAILABILITY OF DATA AND MATERIAL: Not applicable.

Novel interacting proteins identified by tandem affinity purification and mass spectrometry associated with IFITM3 protein during PDCoV infection

Interferon-induced transmembrane 3 (IFITM3) is a membrane-associated protein that exhibits antiviral activities against a wide range of viruses through interactions with other cellular and viral proteins. However, knowledge of the mechanisms of IFITM3 in Porcine deltacoronavirus (PDCoV) infection has been lacking. In this study, we demonstrate that IFN-α treatment induces the upregulation of IFITM3 activity and thus attenuates PDCoV infection. PDCoV replication is inhibited in a dose-dependent manner by IFITM3 overexpression. To clarify the novel roles of IFITM3 during PDCoV infection, proteins that interact with IFITM3 were screened by TAP/MS in an ST cell line stably expressing IFITM3 via a lentivirus. We identified known and novel candidate IFITM3-binding proteins and analyzed the protein complexes using GO annotation, KEGG pathway analysis, and protein interaction network analysis. A total of 362 cellular proteins associate with IFITM3 during the first 24 h post-infection. Of these proteins, the relationship between IFITM3 and Rab9a was evaluated by immunofluorescence colocalization analysis using confocal microscopy. IFITM3 partially colocalized with Rab9a and Rab9a exhibited enhanced colocalization following PDCoV infection. We also demonstrated that IFITM3 interacts specifically with Rab9a. Our results considerably expand the protein networks of IFITM3, suggesting that IFITM3 participates in multiple cellular processes during PDCoV infection.

RNA-Seq Analysis of Glycolysis Regulation of Avian Leukosis Virus Subgroup J Replication

Avian Leukosis virus (ALV) is a widely spread virus that causes major economic losses to the global poultry industry. This study aims to investigate the effect of glycolysis on the replication of the ALV-J virus and identify the key circular RNAs that regulate the replication of the ALV-J virus. We found that glucose uptake, pyruvate content, and lactate content in DF1 cells were increased after ALV-J infection. Moreover, inhibiting the glycolysis of ALV-J-infected DF1 cells reduced the replication of the ALV-J virus. To further study the mechanism of glycolysis in the replication of the ALV-J virus, we performed RNA-seq on ALV-J-infected and ALV-J-infected cells treated with glycolysis inhibition. RNA-seq results show that a total of 10,375 circular RNAs (circRNAs) were identified, of which the main types were exonic circular RNAs, and 28 circRNAs were differentially expressed between ALV-J-infected and ALV-J-infected cells treated with glycolysis inhibition. Then, we performed functional enrichment analysis of differentially expressed circRNA source and target genes. Functional enrichment analysis indicated that some circRNAs might be involved in regulating the replication of the ALV-J virus by influencing some pathways like glycolysis/gluconeogenesis, the NOD-like receptor signaling pathway, MAPK signaling pathway, p53 signaling pathway, Toll-like receptor signaling pathway, Insulin signaling pathway, and Apoptosis. This study revealed the effect of glycolysis on the replication of the ALV-J virus in DF1 cells and its possible regulatory mechanism, which provided a basis for understanding the factors influencing the replication of the ALV-J virus and reducing the rate of infection of the ALV-J virus in poultry.

Sialic acids as attachment factors in mosquitoes mediating Japanese encephalitis virus infection

The role of Culex mosquitoes in the transmission of Japanese encephalitis virus (JEV) is crucial, yet the mechanisms of JEV infection in these vectors remain unclear. Previous research has indicated that various host factors participate in JEV infection. Herein, we present evidence that mosquito sialic acids enhance JEV infection both in vivo and in vitro. By treating mosquitoes and C6/36 cells with neuraminidase or lectin, the function of sialic acids is effectively blocked, resulting in significant inhibition of JEV infection. Furthermore, knockdown of the sialic acid biosynthesis genes in Culex mosquitoes also leads to a reduction in JEV infection. Moreover, our research revealed that sialic acids play a role in the attachment of JEV to mosquito cells, but not in its internalization. To further explore the mechanisms underlying the promotion of JEV attachment by sialic acids, we conducted immunoprecipitation experiments to confirm the direct binding of sialic acids to the last α-helix in JEV envelope protein domain III. Overall, our study contributes to a molecular comprehension of the interaction between mosquitoes and JEV and offers potential strategies for preventing the dissemination of flavivirus in natural environments.IMPORTANCEIn this study, we aimed to investigate the impact of glycoconjugate sialic acids on mosquito infection with Japanese encephalitis virus (JEV). Our findings demonstrate that sialic acids play a crucial role in enhancing JEV infection by facilitating the attachment of the virus to the cell membrane. Furthermore, our investigation revealed that sialic acids directly bind to the final α-helix in the JEV envelope protein domain III, thereby accelerating virus adsorption. Collectively, our results highlight the significance of mosquito sialic acids in JEV infection within vectors, contributing to a better understanding of the interaction between mosquitoes and JEV.