MOESM1 of MicroRNA expression profiling of goat peripheral blood mononuclear cells in response to peste des petits ruminants virus infection

Additional file 1. Flow chart of the miRNA prediction and differentially expressed (DE) miRNA analysis from goat PBMC infected with PPRV at 1.0 multiplicity of infection (MOI). The 49nt sequence tags from Hiseq sequencing will go through the data cleaning analysis first, then the standard analysis will annotate the clean tags into different categories and take those which cannot be annotated to any category to predict the novel miRNA and seed edit of potential known miRNA. After getting miRNA result, target prediction for miRNA and GO enrichment and KEGG pathway for target genes will be analyzed

MOESM6 of MicroRNA expression profiling of goat peripheral blood mononuclear cells in response to peste des petits ruminants virus infection

Additional file 6. KEGG analysis of target genes annotated for miRNA differentially expressed in mock- and PPRV-infected goat PBMC. KEGG pathway annotation revealed that 10 364 background genes were annotated for 317 biological processes

MOESM2 of MicroRNA expression profiling of goat peripheral blood mononuclear cells in response to peste des petits ruminants virus infection

Additional file 2. Summary of deep sequencing data for small RNA (sRNA) in mock- and PPRV-infected goat PBMC. A total of 30 573 869 and 30 644 798 clean reads were obtained from the uninfected and infected groups, respectively. The clean reads were annotated and classified as snRNA, rRNA, snoRNA, Rfam other sncRNA, precursor miRNA, mature miRNA, intergenic, intron, exon, and repeats

MOESM5 of MicroRNA expression profiling of goat peripheral blood mononuclear cells in response to peste des petits ruminants virus infection

Additional file 5. WEGO analysis of target genes annotated for DEmiRNA in mock- and PPRV-infected goat PBMC. WEGO analysis showed that a total of 12 065 target genes were successfully annotated for 103 known miRNA and 213 novel miRNA differentially expressed in two groups

MOESM3 of MicroRNA expression profiling of goat peripheral blood mononuclear cells in response to peste des petits ruminants virus infection

Additional file 3. Details of differentially expressed known and novel microRNA (miRNA) in PPRV- versus mock-infected goat PBMC. A total of 316 miRNA (including 103 known miRNA and 213 novel miRNA) were differentially expressed in mock- and PPRV-infected groups. Among these 316 DEmiRNA, 147 miRNA were upregulated and 169 miRNA were downregulated in the PPRV-infected cells compared to the mock-infected cells

MOESM4 of MicroRNA expression profiling of goat peripheral blood mononuclear cells in response to peste des petits ruminants virus infection

Additional file 4. Differentially expressed miRNA in the PPRV-infected goat PBMC compared to the mock-infected groups. Prediction of 12 065 target genes for 103 known miRNA and 213 novel miRNA differentially expressed in the mock-infected and PPRV-infected goat PBMC

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

<p>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.</p

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.</p