Atopic dermatitis (AD), an inflammatory skin disease, exhibits increased incidence with autism spectrum disorders (ASD) in children. However, the mechanism underlying the ASD-AD comorbidity remains unclear. Here, we integrated the metagenomic and metabolomics analysis to characterize the compositions and functional profiles of gut microbiome in ASD children with AD. We found significant alteration in the composition of the intestinal microbial species between ASD-AD group and ASD group based on beta diversity analysis. LEfSe analysis showed tyzzerella_nexilis, eubacterium_sp_OM08_24 and clostridium_nexile_CAG348 were significantly increased in ASD children with AD. In addition, metabolite profiles showed that differentially expressed metabolites were mainly lipids and organic acids. Meanwhile, functional profiles showed that the pathway of cholesterol metabolism and biosynthesis of unsaturated fatty acids was abundant in ASD children with AD. Furthermore, the correlation analysis revealed that bacteroides_sp_CAG443, limosilactobacillus_mucosae had a positive correlation with traumatic acid and ricinoleic acid that were decreased in ASD-AD group, respectively. Eubacterium_ramulus and lachnospiraceae_bacterium were positively correlated with 11,14-eicosadienoic acid (EDA). Taken together, our results propose that altered gut microbiota regulates metabolites to affect the development of atopic dermatitis in ASD children.

Gut microbial dysbiosis and its derived-metabolites changes have been evidenced to participant in diarrhea piglets; little is known underlying the crosstalk between gut microbiota and metabolites in pregnant sow diarrhea induced with PEDV. In this study, we performed fecal metagenomic and metabolomic profiling in diarrheic pregnant sows infected with PEDV to evaluate the functional characteristics of gut microbiota and metabolites. Microbiome analysis revealed the alterations in composition and diversity of gut microbiota in diarrheic pregnant sows compared with non-diarrheic. The relative abundances of the genera Prevotella, Treponema and Bacteroides were significantly lower and the abundant of Lactobacillus and Ruminococcus were increased in diarrheic pregnant sows. In addition, we found that the increase of Ruminococcus_sp_CAG563, Mycoplasma_sp_CAG472, Prevotella_sp_CAG520, Candidatus_Melainabacteria_bacterium and Eubacterium_coprostanoligenes was the important characteristics in diarrheic pregnant sows. In addition, metabolomic analysis showed a distinct metabolic profile in diarrheic pregnant sows infected with PEDV and the differential metabolites were associated with secondary bile acid biosynthesis, protein digestion and absorption, amino acid biosynthesis. Moreover, our multi-omics data integration analysis indicated that the significant dominant bacteria in diarrheic pregnant sows were positively correlated with 5-aminovaleric acid, pantothenate, 8,4-oxyneolignan-4-xyloside and xanthine, while the predominant coexistence of Treponema, Bacteroides, and Fibrobacter promoted the production of dodecanedioic acid, sesamol and sebacic acid in non-diarrheic pregnant sows infected with PEDV. Taken together, our findings revealed the dynamic changes in the microbiota and metabolites of diarrheic pregnant sows during PEDV infection, identifying microbiota‑derived metabolites associated with host resistance, providing novel insight into the host–gut microbiota interaction.

Porcine epidemic diarrhea virus (PEDV) infection leads to serious intestinal disease in piglets, often leading to high mortality rates and substantial economic losses. Understanding host-PEDV interactions is crucial for PEDV therapeutic strategies. N6-methyladenosine (m6A) methylation has been proven to play an important role in host antiviral immunity. However, transcriptome-wide profiling patterns and the biological functions of host m6A methylation in response to PEDV infection remain incompletely understood. This study first observed significant upregulation of m6A regulators (METTL3, FTO, WTAP, YTHDC1, and YTHDF2) in PEDV infection. Following transcriptome-wide m6A methylation and gene expression profiling, this study identified 803 differentially methylated peaks with 674 differentially expressed m6A-methylated genes and 345 differentially expressed genes (DEGs) after PEDV infection. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these differentially methylated genes were enriched mainly in lysine degradation, histidine metabolism, and the ubiquitin-mediated proteolysis pathway, whereas these DEGs were enriched in negative regulation of viral genome replication, viral protein interaction with cytokines and cytokine receptors, nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling, and immune response-related signaling pathways. Furthermore, the joint analysis of RNA sequencing (RNA-seq) and methylated RNA immunoprecipitation sequencing (MeRIP-seq) identified 16 differentially expressed genes with m6A methylation (AMDHD1, CPM, DCTPP1, GIMAP1, GVIN1, HERC6, LOC100522040, LOC106510546, NFAT5, PIM3, PPARGC1B, RASSF2, SAPCD2, URB2, XRRA1, and ZC3HAV1L), which were associated with immune response and metabolism. Taken together, the study results map the dynamic landscape of host m6A methylation and demonstrate the functional enrichment of m6A methylated genes during PEDV infection, thereby providing a theoretical framework for future research on the role of m6A methylation in resistance to PEDV infection.

Glaesserella parasuis (GPS) infection causes severe inflammatory disorder, resulting in lung injury. SIRT7 is an NAD+-dependent deacetylase known to regulate inflammatory responses, but its role in GPS infection remains unclear. Here we found that GPS infection increased SIRT7 expression and induced inflammatory responses. Deficiency of SIRT7 by CRISPR/Cas9 technology significantly inhibited GPS-induced cytopathic effects and inflammatory responses. In addition, RNA-seq analysis showed that differentially expressed genes(DEGs) induced by SIRT7 deficiency were enriched in biological processes such as cell proliferation, actin cytoskeleton formation, lipid synthesis, protein kinase activation regulation, and GTPase activity regulation. Functional enrichment analysis further indicated the involvement of these DEGs in tight junction pathway, PI3K-Akt signaling pathway, actin cytoskeleton regulation, cGMP-PKG signaling pathway, Hippo signaling pathway, and TNF signaling pathway. Finally, we identified some hub genes (GNAI3, GNAI1, JAK1, NDUFS8, CYC1) related to oxidative phosphorylation. In summary, our results demonstrate that SIRT7 is pivotal for GPS-induced inflammatory responses, which represents a promising target resistant to GPS infection.

Influenza pandemic with H1N1 (H1N1pdms) causes severe lung damage and “cytokine storm,” leading to higher mortality and global health emergencies in humans and animals. Explaining host antiviral molecular mechanisms in response to H1N1pdms is important for the development of novel therapies. In this study, we organised and analysed multimicroarray data for mouse lungs infected with different H1N1pdm and nonpandemic H1N1 strains. We found that H1N1pdms infection resulted in a large proportion of differentially expressed genes (DEGs) in the infected lungs compared with normal lungs, and the number of DEGs increased markedly with the time of infection. In addition, we found that different H1N1pdm strains induced similarly innate immune responses and the identified DEGs during H1N1pdms infection were functionally concentrated in defence response to virus, cytokine-mediated signalling pathway, regulation of innate immune response, and response to interferon. Moreover, comparing with nonpandemic H1N1, we identified ten distinct DEGs (AREG, CXCL13, GATM, GPR171, IFI35, IFI47, IFIT3, ORM1, RETNLA, and UBD), which were enriched in immune response and cell surface receptor signalling pathway as well as interacted with immune response-related dysregulated genes during H1N1pdms. Our discoveries will provide comprehensive insights into host responding to pandemic with influenza H1N1 and find broad-spectrum effective treatment.

MicroRNAs (miRNAs) are important regulators of gene expression and are involved in bacterial pathogenesis and host-pathogen interactions. In this study, we investigated the function of miRNAs in the regulation of host responses to Pasteurella multocida infection. Using next-generation sequencing, we analyzed miRNA expression pattern and identified differentially expressed miRNAs in Pasteurella multocida-infected goat lungs. In addition, we investigated the function of differentially expressed miRNAs andtheir targeted signaling pathways in bacterial infection processes. The results showed that Pasteurella multocida infection led to 69 significantly differentially expressed miRNAs, including 28 known annotated miRNAs with miR-497-3p showing the most significant difference. Gene target prediction and functional enrichment analyses showed that the target genes were mainly involved in cell proliferation, regulation of the cellular metabolic process, positive regulation of cellular process, cellular senescence, PI3K-Akt signaling pathway, FoxO signaling pathway and infection-related pathways. In conclusion, these data provide a new perspective on the roles of miRNAs in Pasteurella multocida infection.

The influenza virus induces cellular apoptosis during viral propagation, and controlling this virus-induced apoptosis process has been shown to have significant antiviral effects. The proapoptotic BH3-only protein Noxa is a strong inducer of apoptosis that can be activated by this virus, suggesting that Noxa has the potential as an anti-influenza target. To assess the value of Noxa as an antiviral target, we utilized CRISPR/Cas9 technology to produce a Noxa-knockout cell line. We found that the knockout of Noxa resulted in a dramatic reduction in the cytopathic effect induced by the influenza virus. Moreover, Noxa knockout decreased the expression of influenza viral proteins (NP, M2, HA, and NS2). In addition, Noxa deficiency triggered a complete autophagic flux to weaken influenza virus-induced autophagosome accumulation, indicating that Noxa may be a promising antiviral target for controlling influenza virus infections.

Influenza A virus (IAV) is an infectious pathogen, threatening the population and public safety with its epidemics. Therefore, it is essential to better understand influenza virus biology to develop efficient strategies against its pathogenicity. Autophagy is an important cellular process to maintain cellular homeostasis by cleaning up the hazardous substrates in lysosome. Accumulating research has also suggested that autophagy is a critical mechanism in host defense responses against IAV infection by degrading viral particles and activating innate or acquired immunity to induce viral clearance. However, IAV has conversely hijacked autophagy to strengthen virus infection by blocking autophagy maturation and further interfering host antiviral signalling to promote viral replication. Therefore, how the battle for autophagy between host and IAV is carried out need to be known. In this review, we describe the role of autophagy in host defence and IAV survival, and summarize the role of influenza proteins in subverting the autophagic process as well as then concentrate on how host utilize antiviral function of autophagy to prevent IAV infection.

BackgroundTNK2/ACK1, a non-receptor tyrosine kinase, plays critical roles in signalling transduces and trafficking. Our previous genome-wide CRISPR/CAS9 knockout screen revealed that mutant of TNK2 produced more restrict to influenza virus infection. In this study, we aim to illustrate the role of TNK2 for influenza A virus (IAV) replication in human cells.ResultsCRISPR/Cas9-mediated mutant of TNK2 resulted in a significant reduction in viral proteins expression and viral titres for multiple influenza strains, and furthermore, a decrease of nuclear import of IAV in the infected TNK2 mutant cells was observed in 3h post-infection. Interestingly, TNK2 mutation enhanced the colocalization of LC3 with autophagic receptor p62 and led to the attenuation of influenza virus-caused accumulation of autophagosomes in TNK2 mutant cells. Further, confocal microscopy visualization result showed that influenza viral matrix 2 (M2) was colocalized with Lamp1 in the infected TNK2 mutant cells in early infection, while almost no colocalization between M2 and Lamp1 was observed in IAV-infected wild-type cells. Moreover, TNK2 depletion also affected the trafficking of early endosome and the movement of influenza viral NP and M2.ConclusionsOur results identified TNK2 as a critical host factor for influenza viral M2 protein trafficking, suggesting that TNK2 will be an attractive target for the development of antivirals therapeutics.

Haemophilus parasuis (H.parasuis), an important swine pathogen, causes Glässer's disease leading to pulmonary fibrosis, polyserositis, meningitis, and arthritis. However, the common molecular response and reaction from the host remain unknown. In this study, to uncover novel host factors involved in H.parasuis infection, we identified the global transcriptomics of porcine lung, spleen, blood, alveolar macrophages (PAM), peripheral blood mononuclear cell (PBMC) and aortic vascular endothelial cells (PAVECs) after infection of H.parasuis (Hps0165 strains) using microarray data and high throughput sequencing from Gene Expression Omnibus (GEO), respectively. The results showed that fifteen overlapped genes were significantly regulated in H.parasuis infected porcine lung and spleen, and then were compared with the data from porcine blood, revealing RETN, TIMP1 and C4BPA play potentially an important role for H.parasuis invasion. Furthermore, through analysing porcine cells infected with H.parasuis, we uncover the only overlap gene TIMP1 remarkably upregulated in all assembled data, indicating that TIMP1 could function as key target for the treatment of H.parasuis infection.

Avian and human influenza viruses bind to porcine sialic acid receptors to generate novel viruses that pose a potential pandemic threat to public health. Evidence suggests that the host factors regulating the influenza virus life cycle and viral reassortment are potential broad-spectrum antiviral drug targets, compared to the ineffective seasonal vaccines against highly pathogenic viruses, leading to drug resistance. After performing a genome-wide CRISPR-Cas9 screen targeting 13,735 genes in porcine cell lines, we identified several host factors critical for influenza virus infection-notably, a conserved oligomeric Golgi complex protein, COG8, which regulates viral protein transport and immune factor expression. Viral titers indicated that the loss of COG8 significantly enhanced cellular resistance to influenza (p < 0.005). Moreover, COG8 knockout reduced the colocalization between viral particles and early endosome marker (EEA1), indicating COG8's role in the early endosome trafficking events of the virus. COG8 deletion inhibited the retrograde transport from the endosome to the trans-Golgi network, thereby accumulating the influenza protein M2 in early endosomes. COG8 silencing enhanced the expression of immune-related genes, indicating COG8-mediated host immune responses affect virus replication. Our experiments have revealed COG8 as an essential factor in influenza virus infection.

Influenza A virus (IAV) has a higher genetic variation, leading to the poor efficiency of traditional vaccine and antiviral strategies targeting viral proteins. Therefore, developing broad-spectrum antiviral treatments is particularly important. Host responses to IAV infection provide a promising approach to identify antiviral factors involved in virus infection as potential molecular drug targets. In this study, in order to better illustrate the molecular mechanism of host responses to IAV and develop broad-spectrum antiviral drugs, we systematically analyzed mRNA expression profiles of host genes in a variety of human cells, including transformed and primary epithelial cells infected with different subtypes of IAV by mining 35 microarray datasets from the GEO database. The transcriptomic results showed that IAV infection resulted in the difference in expression of amounts of host genes in all cell types, especially those genes participating in immune defense and antiviral response. In addition, following the criteria of P<0.05 and |logFC|≥1.5, we found that some difference expression genes were overlapped in different cell types under IAV infection via integrative gene network analysis. IFI6, IFIT2, ISG15, HERC5, RSAD2, GBP1, IFIT3, IFITM1, LAMP3, USP18, and CXCL10 might act as key antiviral factors in alveolar basal epithelial cells against IAV infection, while BATF2, CXCL10, IFI44L, IL6, and OAS2 played important roles in airway epithelial cells in response to different subtypes of IAV infection. Additionally, we also revealed that some overlaps (BATF2, IFI44L, IFI44, HERC5, CXCL10, OAS2, IFIT3, USP18, OAS1, IFIT2) were commonly upregulated in human primary epithelial cells infected with high or low pathogenicity IAV. Moreover, there were similar defense responses activated by IAV infection, including the interferon-regulated signaling pathway in different phagocyte types, although the differentially expressed genes in different phagocyte types showed a great difference. Taken together, our findings will help better understand the fundamental patterns of molecular responses induced by highly or lowly pathogenic IAV, and the overlapped genes upregulated by IAV in different cell types may act as early detection markers or broad-spectrum antiviral targets.

Influenza A virus (IAV) has the higher genetic variation and reassortment, the traditional vaccine and virus-directed antiviral strategies have hardly shown successful efficacy and even lead to serious resistance, therefor developing the broad-spectrum antiviral treatments is particularly important. Host response to IAV infection provides a promising alternative approach to find host factors that are involved in the replication of viruses as molecular drug target. In this study, in order to better illustrate how IAV infection triggers cellular response and understand virus-host interaction, we systematically studied the expression profiles of host gene in a variety of human cells (including epithelial cells, primary epithelial cells) infected with different subtypes of IAV in this research by collecting and excavating 40 microarray data from Gene Expression Omnibus (GEO). The transcriptome analysis results showed that each of influenza strains led to the certain amounts of genes differentially regulated in all cell types, especially those genes belonging to immune defense and antiviral response, but we found that the overlapping regulated genes accounted for only a few in all cell types with different subtypes of IAV infection following the the criteria of P<0.05 and |logFC|≥1.5, because of the difference of IAV strains and infected cell types. Integrative gene network analysis found that IFI6, IFIT2, ISG15, HERC5, RSAD2, GBP1, IFIT3, IFITM1, LAMP3, USP18 and CXCL10 may act as key signatures in alveolar basal epithelial cells for IAV infection, while BATF2, CXCL10, IFI44L, IL6 and OAS2 played a key role in airway epithelial cell response to different subtypes of IAV infection. In addition, we also revealed that some overlaps (BATF2, IFI44L, IFI44, HERC5, OASL, CXCL10, MX2, OAS2, XAF1, IFIT3, USP18, IFIH1, OAS1, IFIT2 and IFIT1) were commonly upregulated in human primary epithelial cells infected by different influenza strains of high or low pathogenicity. Additionally, in the phagocytes, the difference gene expression pattern in different subtypes of IAV infection was found, but phagocytes could elicit the similar defence response against virus infection. Our findings will help us understand the fundamental patterns of molecular responses induced by highly or lowly pathogenic IAV originating from different species and the overlapped genes upregulated by IAV in different cell types may be as key biomarkers to improve effective early detection and treatment.Funding Statement: This work was supported by Key Lab of Process Analysis and Control of Sichuan Universities (No.2018001), The Project-sponsored by Sichuan Province for ROCS (0903/00021728) and NSFC (81902073).Declaration of Interests: No potential conflict of interest was reported by the authors.