Binding and entry of peste des petits ruminants virus into caprine endometrial epithelial cells profoundly affect early cellular gene expression

Activation of the MKK3-p38-MK2-ZFP36 Axis by Coronavirus Infection Restricts the Upregulation of AU-Rich Element-Containing Transcripts in Proinflammatory Responses

Coronavirus infections induce the expression of multiple proinflammatory cytokines and chemokines. We have previously shown that in cells infected with gammacoronavirus infectious bronchitis virus (IBV), interleukin 6 (IL-6), and IL-8 were drastically upregulated, and the MAP kinase p38 and the integrated stress response pathways were implicated in this process. In this study, we report that coronavirus infection activates a negative regulatory loop that restricts the upregulation of a number of proinflammatory genes. As revealed by the initial transcriptomic and subsequent validation analyses, the anti-inflammatory adenine-uridine (AU)-rich element (ARE)-binding protein, zinc finger protein 36 (ZFP36), and its related family members were upregulated in cells infected with IBV and three other coronaviruses, alphacoronaviruses porcine epidemic diarrhea virus (PEDV), human coronavirus 229E (HCoV-229E), and betacoronavirus HCoV-OC43, respectively. Characterization of the functional roles of ZFP36 during IBV infection demonstrated that ZFP36 promoted the degradation of transcripts coding for IL-6, IL-8, dual-specificity phosphatase 1 (DUSP1), prostaglandin-endoperoxide synthase 2 (PTGS2) and TNF-α-induced protein 3 (TNFAIP3), through binding to AREs in these transcripts. Consistently, knockdown and inhibition of JNK and p38 kinase activities reduced the expression of ZFP36, as well as the expression of IL-6 and IL-8. On the contrary, overexpression of mitogen-activated protein kinase kinase 3 (MKK3) and MAPKAP kinase-2 (MK2), the upstream and downstream kinases of p38, respectively, increased the expression of ZFP36 and decreased the expression of IL-8. Taken together, this study reveals an important regulatory role of the MKK3-p38-MK2-ZFP36 axis in coronavirus infection-induced proinflammatory response. IMPORTANCE Excessive and uncontrolled induction and release of proinflammatory cytokines and chemokines, the so-called cytokine release syndrome (CRS), would cause life-threatening complications and multiple organ failure in severe coronavirus infections, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and COVID-19. This study reveals that coronavirus infection also induces the expression of ZFP36, an anti-inflammatory ARE-binding protein, promoting the degradation of ARE-containing transcripts coding for IL-6 and IL-8 as well as a number of other proteins related to inflammatory response. Furthermore, the p38 MAP kinase, its upstream kinase MKK3 and downstream kinase MK2 were shown to play a regulatory role in upregulation of ZFP36 during coronavirus infection cycles. This MKK3-p38-MK2-ZFP36 axis would constitute a potential therapeutic target for severe coronavirus infections.

Quantitative Proteomics Reveals a Novel Role of the E3 Ubiquitin-Protein Ligase FANCL in the Activation of the Innate Immune Response through Regulation of TBK1 Phosphorylation during Peste des Petits Ruminants Virus Infection

Peste des petits ruminants virus (PPRV) infection causes considerable innate immunosuppression in its host, which promotes viral replication. However, how the host rescues the innate immune response to counteract this immunosuppression during viral replication remains largely unknown. To explore the mechanisms of how a host counteracts PPRV-mediated innate immunosuppression, a high-throughput quantitation proteomic approach (isobaric tags for relative and absolute quantitation in conjunction with LC-MS/MS) was used to investigate the proteome landscape of goat fetal fibroblasts (GFFs) in response to PPRV infection. Eventually, 497 upregulated proteins and 358 downregulated proteins were identified. Many of the differentially expressed proteins were enriched in immune-related pathways. Blocking the activation of the innate immune response with a specific inhibitor BX795 in GFFs remarkably promoted PPRV replication, suggesting the significant antiviral role of the enriched immune-related pathways. The GO enrichment analysis showed that the host protein FANCL revealed a similar expression pattern to these innate immune-related proteins. In addition, the analysis of protein-protein interaction networks reveals a potential relationship between FANCL and the innate immune pathway. We determined that FANCL inhibited PPRV infection by enhancing type I interferon (IFN) and IFN-stimulated gene expression. Further investigation determined that FANCL induced type I IFN production by promoting TBK1 phosphorylation, thus impairing PPRV-mediated immunosuppression.

Interactions Among Expressed MicroRNAs and mRNAs in the Early Stages of Fowl Adenovirus Aerotype 4-Infected Leghorn Male Hepatocellular Cells

Hydropericardium-hepatitis syndrome (HHS) is caused by some strains of fowl adenovirus serotype 4 (FAdV-4). However, the mechanism of FAdV-4 entry is not well understood. Therefore, to investigate the changes in host cellular response at the early stage of FAdV-4 infection, a conjoint analysis of miRNA-seq and mRNA-seq was utilized with leghorn male hepatocellular (LMH) cells at 30, 60, and 120 min after FAdV-4 infection. In total, we identified 785 differentially expressed (DE) miRNAs and 725 DE mRNAs in FAdV-4-infected LMH cells. Most miRNAs and mRNAs, including gga-miR-148a-3p, gga-miR-148a-5p, gga-miR-15c-3p, CRK, SOCS3, and EGR1, have not previously been reported to be associated with FAdV-4 infection. The conjoint analysis of the obtained data identified 856 miRNA–mRNA pairs at three time points. The interaction network analysis showed that gga-miR-128-2-5p, gga-miR-7475-5p, novel_miR205, and TCF7L1 were located in the core of the network. Furthermore, the relationship between gga-miR-128-2-5p and its target OBSL1 was confirmed using a dual-luciferase reporter system and a real-time quantitative polymerase chain reaction assay. In vitro experiments revealed that both gga-miR-128-2-5p overexpression and OBSL1 loss of function inhibited FAdV-4 entry. These results suggested that gga-miR-128-2-5p plays an important role in FAdV-4 entry by targeting OBSL1. To the best of our knowledge, the present study is the first to analyze host miRNA and mRNA expression at the early stage of FAdV-4 infection; furthermore, the results of this study help to elucidate the molecular mechanisms of FAdV-4 entry.

Microarray-Based Quality Assessment as a Supporting Criterion for de novo Transcriptome Assembly Selection

RNA-Sequencing and de novo assembly have enabled the analysis of species with non-available reference transcriptomes, although intrinsic features (biological and technical) induce errors in the reconstruction. A strategy to resolve these errors consists of varying assembling process parameters to generate multiple reconstructions. However, the best assembly selection remains a challenge. Quantitative metrics for quality assessment have been inconsistent when compared with pertinent references. In this paper, a criterion for supporting assembly selection based on mapping DNA microarray hybridized probes to assembly sets is proposed. Mouse and fruit fly RNA-Seq datasets were assembled with standard de novo procedures. Quality assessment was estimated using quantitative metrics and the proposed criterion. The assembly that best mapped to the available reference transcriptomes of these model species provided the highest quality assembly. The hybridized probes identified the best assemblies, whereas quantitative metrics remained inconsistent. For example, subtle probe mapping difference of 0.25 percent, but statistically significant (ANOVA, p < 0.05), enabled the assembly selection that led to identify 3,719 more contigs and led to 1,049 further mapped contigs to the mouse reference transcriptome. The microarray data availability for non-model species makes the proposed criterion suitable for quality assessment of multiple de novo assembly strategies.

MicroRNA-218 Regulates Signaling Lymphocyte Activation Molecular (SLAM) Mediated Peste des Petits Ruminants Virus Infectivity in Goat Peripheral Blood Mononuclear Cells

Peste des petits ruminants virus (PPRV) has emerged as a significant threat to the productivity of small ruminants worldwide. SLAM was identified as the primary receptor for PPRV and other Morbilliviruses, although the regulation of SLAM expression is not yet fully understood. In this study, we revealed a novel mechanism by which PPRV upregulates its receptor SLAM expression and thereby benefits its replication via suppressing miR-218, a novel negative miRNA directly targeting SLAM gene. We demonstrated that PPRV infection downregulates miR-218, which in turn enhances SLAM expression on the surface of goat peripheral blood mononuclear cells (PBMCs), thus promoting PPRV replication. Since SLAM signaling may modulate the immune responses induced by PPRV infection, we further examined the effect of SLAM expression on the production of various cytokines by PBMCs in the absence or presence of PPRV. We demonstrated that miR-218-mediated SLAM expression modulates the expression of IFN-γ, TNF-α, and IL-10, importantly, these modulatory effects were enhanced in the presence of PPRV infection. Furthermore, our data clearly showed that PPRV H protein is sufficient to regulate miR-218-mediated SLAM expression. Taken together, our results suggest a novel mechanism involving post-transcriptional regulation of SLAM receptor expression on goat PBMCs during PPRV infection.

Host Cellular Receptors for the Peste des Petits Ruminant Virus

Peste des Petits Ruminant (PPR) is an important transboundary, OIE-listed contagious viral disease of primarily sheep and goats caused by the PPR virus (PPRV), which belongs to the genus Morbillivirus of the family Paramyxoviridae. The mortality rate is 90–100%, and the morbidity rate may reach up to 100%. PPR is considered economically important as it decreases the production and productivity of livestock. In many endemic poor countries, it has remained an obstacle to the development of sustainable agriculture. Hence, proper control measures have become a necessity to prevent its rapid spread across the world. For this, detailed information on the pathogenesis of the virus and the virus host interaction through cellular receptors needs to be understood clearly. Presently, two cellular receptors; signaling lymphocyte activation molecule (SLAM) and Nectin-4 are known for PPRV. However, extensive information on virus interactions with these receptors and their impact on host immune response is still required. Hence, a thorough understanding of PPRV receptors and the mechanism involved in the induction of immunosuppression is crucial for controlling PPR. In this review, we discuss PPRV cellular receptors, viral host interaction with cellular receptors, and immunosuppression induced by the virus with reference to other Morbilliviruses.

Autophagy induction by the pathogen receptor NECTIN4 and sustained autophagy contribute to peste des petits ruminants virus infectivity

Macroautophagy/autophagy is an essential cellular response in the fight against intracellular pathogens. Although some viruses can escape from or utilize autophagy to ensure their own replication, the responses of autophagy pathways to viral invasion remain poorly documented. Here, we show that peste des petits ruminants virus (PPRV) infection induces successive autophagic signalling in host cells via distinct and uncoupled molecular pathways. Immediately upon invasion, PPRV induced a first transient wave of autophagy via a mechanism involving the cellular pathogen receptor NECTIN4 and an AKT-MTOR-dependent pathway. Autophagic detection showed that early PPRV infection not only increased the amounts of autophagosomes and LC3-II but also downregulated the phosphorylation of AKT-MTOR. Subsequently, we found that the binding of viral protein H to NECTIN4 ultimately induced a wave of autophagy and inactivated the AKT-MTOR pathway, which is a critical step for the control of infection. Soon after infection, new autophagic signalling was initiated that required viral replication and protein expression. Interestingly, expression of IRGM and HSPA1A was significantly upregulated following PPRV replication. Strikingly, knockdown of IRGM and HSPA1A expression using small interfering RNAs impaired the PPRV-induced second autophagic wave and viral particle production. Moreover, IRGM-interacting PPRV-C and HSPA1A-interacting PPRV-N expression was sufficient to induce autophagy through an IRGM-HSPA1A-dependent pathway. Importantly, syncytia formation could facilitate sustained autophagy and the replication of PPRV. Overall, our work reveals distinct molecular pathways underlying the induction of self-beneficial sustained autophagy by attenuated PPRV, which will contribute to improving the use of vaccines for therapy.

Abbreviations: ACTB: actin beta; ANOVA: analysis of variance; ATG: autophagy-related; BECN1: beclin 1; CDV: canine distemper virus; Co-IP: coimmunoprecipitation; FIP: fusion inhibitory peptide; GFP: green fluorescent protein; GST: glutathione S-transferase; HMOX1: heme oxygenase 1; hpi: hours post infection; HSPA1A: heat shock protein family A (Hsp70) member 1A; HSP90AA1: heat shock protein 90 kDa alpha (cytosolic), class A member 1; IFN: interferon; IgG: immunoglobulin G; INS: insulin; IRGM: immunity related GTPase M; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MeV: measles virus; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; PI3K: phosphoinositide-3 kinase; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; SDS: sodium dodecyl sulfate; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; UV: ultraviolet.

Autophagy enhances the replication of Peste des petits ruminants virus and inhibits caspase-dependent apoptosis in vitro

Peste des petits ruminants (PPR) is an acute and highly contagious disease in small ruminants that causes significant economic losses in developing countries. An increasing number of studies have demonstrated that both autophagy and apoptosis are important cellular mechanisms for maintaining homeostasis, and they participate in the host response to pathogens. However, the crosstalk between apoptosis and autophagy in host cells during PPRV infection has not been clarified. In this study, autophagy was induced upon virus infection in caprine endometrial epithelial cells (EECs), as determined by the appearance of double- and single-membrane autophagy-like vesicles, LC3-I/LC3-II conversion, and p62 degradation. We also found that PPRV infection triggered a complete autophagic response, most likely mediated by the non-structural protein C and nucleoprotein N. Moreover, our results suggest that autophagy not only promotes the replication of PPRV in EECs but also provides a potential mechanism for inhibiting PPRV-induced apoptosis. Inhibiting autophagosome formation by wortmannin and knocking down the essential autophagic proteins Beclin-1 and ATG7 induces caspase-dependent apoptosis in EECs in PPRV infection. However, inhibiting autophagosome and lysosome fusion by NH₄Cl and chloroquine did not increase the number of apoptotic cells. Collectively, these data are the first to indicate that PPRV-induced autophagy inhibits caspase-dependent apoptosis and thus contributes to the enhancement of viral replication and maturity in host cells.