Epigenetic changes mediated by microRNA miR29 activate cyclooxygenase 2 and lambda-1 interferon production during viral infection

MicroRNAs and the immune response to respiratory virus infections

MicroRNAs (miRNAs) are small ssRNA molecules, which are involved in gene expression regulation at the post-transcriptional level. Their biological functions include modulation of both innate and adaptive immune response. miRNAs participate in the maintenance of the airway epithelial barrier and are also implicated in the modulation of antiviral defense in epithelial cells. The immune response to respiratory viruses such as rhinovirus, influenza virus and respiratory syncytial virus is associated with an altered expression of distinct miRNAs, and the changes in the miRNA expression profile in epithelial cells may contribute to the pathogenesis of both acute and chronic airway disease. Understanding the role of these small molecules in the antiviral immune response and identification of miRNAs target genes may help to clarify the mechanisms of virus-host interaction, and in the future may lead to development of new antiviral treatments.

Bugs in the system

Immunity to respiratory virus infection is governed by complex biological networks that influence disease progression and pathogenesis. Systems biology provides an opportunity to explore and understand these multifaceted interactions based on integration and modeling of multiple biological parameters. In this review, we describe new and refined systems‐based approaches used to model, identify, and validate novel targets within complex networks following influenza and coronavirus infection. In addition, we propose avenues for extension and expansion that can revolutionize our understanding of infectious disease processes. Together, we hope to provide a window into the unique and expansive opportunity presented by systems biology to understand complex disease processes within the context of infectious diseases.

Systems biology unravels interferon responses to respiratory virus infections

Interferon production is an important defence against viral replication and its activation is an attractive therapeutic target. However, it has long been known that viruses perpetually evolve a multitude of strategies to evade these host immune responses. In recent years there has been an explosion of information on virus-induced alterations of the host immune response that have resulted from data-rich omics technologies. Unravelling how these systems interact and determining the overall outcome of the host response to viral infection will play an important role in future treatment and vaccine development. In this review we focus primarily on the interferon pathway and its regulation as well as mechanisms by which respiratory RNA viruses interfere with its signalling capacity.

Small RNA analysis in Sindbis virus infected human HEK293 cells

INTRODUCTION

In contrast to the defence mechanism of RNA interference (RNAi) in plants and invertebrates, its role in the innate response to virus infection of mammals is a matter of debate. Since RNAi has a well-established role in controlling infection of the alphavirus Sindbis virus (SINV) in insects, we have used this virus to investigate the role of RNAi in SINV infection of human cells.

RESULTS

SINV AR339 and TR339-GFP were adapted to grow in HEK293 cells. Deep sequencing of small RNAs (sRNAs) early in SINV infection (4 and 6 hpi) showed low abundance (0.8%) of viral sRNAs (vsRNAs), with no size, sequence or location specific patterns characteristic of Dicer products nor did they possess any discernible pattern to ascribe to a specific RNAi biogenesis pathway. This was supported by multiple variants for each sequence, and lack of hot spots along the viral genome sequence. The abundance of the best defined vsRNAs was below the limit of Northern blot detection. The adaptation of the virus to HEK293 cells showed little sequence changes compared to the reference; however, a SNP in E1 gene with a preference from G to C was found. Deep sequencing results showed little variation of expression of cellular microRNAs (miRNAs) at 4 and 6 hpi compared to uninfected cells. Twelve miRNAs exhibiting some minor differential expression by sequencing, showed no difference in expression by Northern blot analysis.

CONCLUSIONS

We show that, unlike SINV infection of invertebrates, generation of Dicer-dependent svRNAs and change in expression of cellular miRNAs were not detected as part of the Human response to SINV.

MicroRNA-29b modulates Japanese encephalitis virus-induced microglia activation by targeting tumor necrosis factor alpha-induced protein 3

Japanese encephalitis virus (JEV), a single-stranded RNA (ssRNA) virus, is the leading cause of encephalitis in Asia. Microglial activation is one of the key events in JEV-induced neuroinflammation. Although the various microRNAs (miRNAs) has been shown to regulate microglia activation during pathological conditions including neuroviral infections, till date, the involvement of miRNAs in JEV infection has not been evaluated. Hence, we sought to evaluate the possible role of miRNAs in mediating JEV-induced microglia activation. Initial screening revealed significant up-regulation of miR-29b in JEV-infected mouse microglial cell line (BV-2) and primary microglial cells. Furthermore, using bioinformatics tools, we identified tumor necrosis factor alpha-induced protein 3, a negative regulator of nuclear factor-kappa B signaling as a potential target of miR-29b. Interestingly, in vitro knockdown of miR-29b resulted in significant over-expression of tumor necrosis factor alpha-induced protein 3, and subsequent decrease in nuclear translocation of pNF-κB. JEV infection in BV-2 cell line elevated inducible nitric oxide synthase, cyclooxygenase-2, and pro-inflammatory cytokine expression levels, which diminished after miR-29b knockdown. Collectively, our study demonstrates involvement of miR-29b in regulating JEV- induced microglial activation.

Comparison of influenza A virus infection in high- and low-birth-weight pigs using morphometric analysis

BACKGROUND

Epigenetic studies have shown that low-birth-weight (LBW) and growth restriction has been associated with reduced immune function in humans and reduced passive immunity in pigs. To examine the immune responses of high-birth-weight (HBW) and LBW groups of pigs, influenza A virus infection was used as an exemplifier of neonatal respiratory disease.

OBJECTIVES

The objectives of this study were (i) to compare clinical, immunological, and pathological outcome of influenza infection in HBW to LBW pigs and (ii) to establish standardized sampling sites, score each site independently with set criteria, and compare scores between sites.

METHODS

Sixty-eight 4-week-old pigs originating from either HBW or LBW litters were intratracheally inoculated with 10(6.3) TCID50 /ml of A/swine/Texas/4199-2/1998 H3N2 and euthanized 48 hours later. Samples were collected 2.5 cm from the tip of both cranial and middle lung lobes. The formalin-fixed paraffin-embedded tissue sections were scored in a blinded manner by a single pathologist using established scoring criteria for routine and immunohistochemical stains. Clinical parameters, lung and nasal swab virus titers, and cytokine levels for interferon-alpha and interleukin-1-beta, IL-6, and IL-8 were measured.

RESULTS AND CONCLUSIONS

Lung lesion severity and influenza staining intensity were significantly lower in LBW compared with HBW pigs (P < 0.05). Additionally, examining just the LBW group, the significant difference between lobes (P = 0.009) showed that the mean score for the right cranial lung lobe was higher compared with the other three lobes.

The amazing innate immune response to influenza A virus infection

Influenza A viruses (IAVs) remain a major health threat and a prime example of the significance of innate immunity. Our understanding of innate immunity to IAV has grown dramatically, yielding new concepts that change the way we view innate immunity as a whole. Examples include the role of p53, autophagy, microRNA, innate lymphocytes, endothelial cells and gut commensal bacteria in pulmonary innate immunity. Although the innate response is largely beneficial, it also contributes to major complications of IAV, including lung injury, bacterial super-infection and exacerbation of reactive airways disease. Research is beginning to dissect out which components of the innate response are helpful or harmful. IAV uses its limited genetic complement to maximum effect. Several viral proteins are dedicated to combating innate responses, while other viral structural or replication proteins multitask as host immune modulators. Many host innate immune proteins also multitask, having roles in cell cycle, signaling or normal lung biology. We summarize the plethora of new findings and attempt to integrate them into the larger picture of how humans have adapted to the threat posed by this remarkable virus. We explore how our expanded knowledge suggests ways to modulate helpful and harmful inflammatory responses, and develop novel treatments.

Construction of the influenza A virus infection-induced cell-specific inflammatory regulatory network based on mutual information and optimization

Background

Influenza A virus (IAV) infection-induced inflammatory regulatory networks (IRNs) are extremely complex and dynamic. Specific biological experiments for investigating the interactions between individual inflammatory factors cannot provide a detailed and insightful multidimensional view of IRNs. Recently, data from high-throughput technologies have permitted system-level analyses. The construction of large and cell-specific IRNs from high-throughput data is essential to understanding the pathogenesis of IAV infection.

Results

In this study, we proposed a computational method, which combines nonlinear ordinary differential equation (ODE)-based optimization with mutual information, to construct a cell-specific optimized IRN during IAV infection by integrating gene expression data with a prior knowledge of network topology. Moreover, we used the average relative error and sensitivity analysis to evaluate the effectiveness of our proposed approach. Furthermore, from the optimized IRN, we confirmed 45 interactions between proteins in biological experiments and identified 37 new regulatory interactions and 8 false positive interactions, including the following interactions: IL1β regulates TLR3, TLR3 regulates IFN-β and TNF regulates IL6. Most of these regulatory interactions are statistically significant by Z-statistic. The functional annotations of the optimized IRN demonstrated clearly that the defense response, immune response, response to wounding and regulation of cytokine production are the pivotal processes of IAV-induced inflammatory response. The pathway analysis results from the Kyoto Encyclopaedia of Genes and Genomes (KEGG) showed that 8 pathways are enriched significantly. The 5 pathways were validated by experiments, and 3 other pathways, including the intestinal immune network for IgA production, the cytosolic DNA-sensing pathway and the allograft rejection pathway, are the predicted novel pathways involved in the inflammatory response.

Conclusions

Integration of knowledge-driven and data-driven methods allows us to construct an effective IRN during IAV infection. Based on the constructed network, we have identified new interactions among inflammatory factors and biological pathways. These findings provide new insight into our understanding of the molecular mechanisms in the inflammatory network in response to IAV infection. Further characterization and experimental validation of the interaction mechanisms identified from this study may lead to a novel therapeutic strategy for the control of infections and inflammatory responses.

Target Gene and Function Prediction of Differentially Expressed MicroRNAs in Lactating Mammary Glands of Dairy Goats

MicroRNAs are small noncoding RNAs that can regulate gene expression, and they can be involved in the regulation of mammary gland development. The differential expression of miRNAs during mammary gland development is expected to provide insight into their roles in regulating the homeostasis of mammary gland tissues. To screen out miRNAs that should have important regulatory function in the development of mammary gland from miRNA expression profiles and to predict their function, in this study, the target genes of differentially expressed miRNAs in the lactating mammary glands of Laoshan dairy goats are predicted, and then the functions of these miRNAs are analyzed via bioinformatics. First, we screen the expression patterns of 25 miRNAs that had shown significant differences during the different lactation stages in the mammary gland. Then, these miRNAs are clustered according to their expression patterns. Computational methods were used to obtain 215 target genes for 22 of these miRNAs. Combining gene ontology annotation, Fisher's exact test, and KEGG analysis with the target prediction for these miRNAs, the regulatory functions of miRNAs belonging to different clusters are predicted.

Identification of Host Kinase Genes Required for Influenza Virus Replication and the Regulatory Role of MicroRNAs

Human protein kinases (HPKs) have profound effects on cellular responses. To better understand the role of HPKs and the signaling networks that influence influenza virus replication, a small interfering RNA (siRNA) screen of 720 HPKs was performed. From the screen, 17 HPKs (NPR2, MAP3K1, DYRK3, EPHA6, TPK1, PDK2, EXOSC10, NEK8, PLK4, SGK3, NEK3, PANK4, ITPKB, CDC2L5 (CDK13), CALM2, PKN3, and HK2) were validated as essential for A/WSN/33 influenza virus replication, and 6 HPKs (CDK13, HK2, NEK8, PANK4, PLK4 and SGK3) were identified as vital for both A/WSN/33 and A/New Caledonia/20/99 influenza virus replication. These HPKs were found to affect multiple host pathways and regulated by miRNAs induced during infection. Using a panel of miRNA agonists and antagonists, miR-149* was found to regulate NEK8 expression, miR-548d-3p was found to regulate MAPK1 transcript expression, and miRs -1228 and -138 to regulate CDK13 expression. Up-regulation of miR-34c induced PLK4 transcript and protein expression and enhanced influenza virus replication, while miR-34c inhibition reduced viral replication. These findings identify HPKs important for influenza viral replication and show the miRNAs that govern their expression.

Infection with influenza A viruses causes changes in promoter DNA methylation of inflammatory genes

Background

Replication of influenza virus in the host cells results in production of immune mediators like cytokines. Excessive secretion of cytokines (hypercytokinemia) has been observed during highly pathogenic avian influenza virus (HPAI‐H5N1) infections resulting in high fatality rates.

Objective

The exact mechanism of hypercytokinemia during influenza virus infection is still not known completely. As promoter DNA methylation changes are linked with expression changes in genes, we intend to identify whether changes in promoter DNA methylation have any role in expression of cytokines during influenza A virus infection.

Methods

A panel of 24 cytokine genes and genes known to be involved in inflammatory response were analyzed for their promoter DNA methylation changes during influenza A virus infections. Four different strains of influenza A viruses, viz. H5N1, H1N1, pandemic (2009) H1N1, and a vaccine strain of H5N1, were used for the study.

Results

We found seven of the total 24 inflammatory genes studied, showing significant changes in their promoter methylation levels in response to virus infection. These genes included proinflammatory cytokines CXCL14, CCL25, CXCL6, and interleukines IL13, IL17C, IL4R. The changes in DNA methylation levels varied across different strains of influenza viruses depending upon their virulence. Significant promoter hypomethylation in IL17C and IL13 genes was observed in cells infected with HPAI‐H5N1 virus compared with other influenza viruses. This decrease in methylation was found to be positively correlating with the increased expression of these genes. Analysis of IL17C promoter region using bisulfite sequencing resulted in identification of a CpG site within Retinoid X receptor‐alpha (RXR‐α) transcription factor binding site undergoing demethylation specifically in H5N1‐infected cells but not in other influenza‐infected cells.

Conclusion

Thus, the study could demonstrate that changes in promoter methylation in certain specific cytokine genes actually have a possible role in their expression changes during influenza A virus infection.

Human blood dendritic cell antigen 3 (BDCA3)(+) dendritic cells are a potent producer of interferon-λ in response to hepatitis C virus

The polymorphisms in the interleukin (IL)-28B (interferon-lambda [IFN]-λ3) gene are strongly associated with the efficacy of hepatitis C virus (HCV) clearance. Dendritic cells (DCs) sense HCV and produce IFNs, thereby playing some cooperative roles with HCV-infected hepatocytes in the induction of interferon-stimulated genes (ISGs). Blood dendritic cell antigen 3 (BDCA3)(+) DCs were discovered as a producer of IFN-λ upon Toll-like receptor 3 (TLR3) stimulation. We thus aimed to clarify the roles of BDCA3(+) DCs in anti-HCV innate immunity. Seventy healthy subjects and 20 patients with liver tumors were enrolled. BDCA3(+) DCs, in comparison with plasmacytoid DCs and myeloid DCs, were stimulated with TLR agonists, cell-cultured HCV (HCVcc), or Huh7.5.1 cells transfected with HCV/JFH-1. BDCA3(+) DCs were treated with anti-CD81 antibody, inhibitors of endosome acidification, TIR-domain-containing adapter-inducing interferon-β (TRIF)-specific inhibitor, or ultraviolet-irradiated HCVcc. The amounts of IL-29/IFN-λ1, IL-28A/IFN-λ2, and IL-28B were quantified by subtype-specific enzyme-linked immunosorbent assay (ELISA). The frequency of BDCA3(+) DCs in peripheral blood mononuclear cell (PBMC) was extremely low but higher in the liver. BDCA3(+) DCs recovered from PBMC or the liver released large amounts of IFN-λs, when stimulated with HCVcc or HCV-transfected Huh7.5.1. BDCA3(+) DCs were able to induce ISGs in the coexisting JFH-1-positive Huh7.5.1 cells. The treatments of BDCA3(+) DCs with anti-CD81 antibody, cloroquine, or bafilomycin A1 reduced HCVcc-induced IL-28B release, whereas BDCA3(+) DCs comparably produced IL-28B upon replication-defective HCVcc. The TRIF-specific inhibitor reduced IL-28B release from HCVcc-stimulated BDCA3(+) DCs. In response to HCVcc or JFH-1-Huh7.5.1, BDCA3(+) DCs in healthy subjects with IL-28B major (rs8099917, TT) released more IL-28B than those with IL-28B minor genotype (TG).

CONCLUSION

Human BDCA3(+) DCs, having a tendency to accumulate in the liver, recognize HCV in a CD81-, endosome-, and TRIF-dependent manner and produce substantial amounts of IL-28B/IFN-λ3, the ability of which is superior in subjects with IL-28B major genotype.

Prostaglandin E2-induced changes in alveolar macrophage scavenger receptor profiles differentially alter phagocytosis of Pseudomonas aeruginosa and Staphylococcus aureus post-bone marrow transplant

The effectiveness of hematopoietic stem cell transplantation as a therapy for malignant and nonmalignant conditions is complicated by pulmonary infections. Using our syngeneic bone marrow transplant (BMT) mouse model, BMT mice with a reconstituted hematopoietic system displayed increased susceptibility to Pseudomonas aeruginosa and Staphylococcus aureus. BMT alveolar macrophages (AMs) exhibited a defect in P. aeruginosa phagocytosis, whereas S. aureus uptake was surprisingly enhanced. We hypothesized that the difference in phagocytosis was due to an altered scavenger receptor (SR) profile. Interestingly, MARCO expression was decreased, whereas SR-AI/II was increased. To understand how these dysregulated SR profiles might affect macrophage function, CHO cells were transfected with SR-AI/II, and phagocytosis assays revealed that SR-AI/II was important for S. aureus uptake but not for P. aeruginosa. Conversely, AMs treated in vitro with soluble MARCO exhibited similar defects in P. aeruginosa internalization as did BMT AMs. The 3'-untranslated region of SR-AI contains a putative target region for microRNA-155 (miR-155), and miR-155 expression is decreased post-BMT. Anti-miR-155-transfected AMs exhibited an increase in SR-AI/II expression and S. aureus phagocytosis. Elevated PGE2 has been implicated in driving an impaired innate immune response post-BMT. In vitro treatment of AMs with PGE2 increased SR-AI/II and decreased MARCO and miR-155. Despite a difference in phagocytic ability, BMT AMs harbor a killing defect to both P. aeruginosa and S. aureus. Thus, our data suggest that PGE2-driven alterations in SR and miR-155 expression account for the differential phagocytosis of P. aeruginosa and S. aureus, but impaired killing ultimately confers increased susceptibility to pulmonary infection.

An overview of the highly pathogenic H5N1 influenza virus

Since the first human case of H5N1 avian influenza virus infection was reported in 1997, this highly pathogenic virus has infected hundreds of people around the world and resulted in many deaths. The ability of H5N1 to cross species boundaries, and the presence of polymorphisms that enhance virulence, present challenges to developing clear strategies to prevent the pandemic spread of this highly pathogenic avian influenza (HPAI) virus. This review summarizes the current understanding of, and recent research on, the avian influenza H5N1 virus, including transmission, virulence, pathogenesis, clinical characteristics, treatment and prevention.

African swine fever virus controls the host transcription and cellular machinery of protein synthesis

Throughout a viral infection, the infected cell reprograms the gene expression pattern in order to establish a satisfactory antiviral response. African swine fever virus (ASFV), like other complex DNA viruses, sets up a number of strategies to evade the host's defense systems, such as apoptosis, inflammation and immune responses. The capability of the virus to persist in its natural hosts and in domestic pigs, which recover from infection with less virulent isolates, suggests that the virus displays effective mechanisms to escape host defense systems. ASFV has been described to regulate the activation of several transcription factors, thus regulating the activation of specific target genes during ASFV infection. Whereas some reports have concerned about anti-apoptotic ASFV genes and the molecular mechanisms by which ASFV interferes with inducible gene transcription and immune evasion, less is yet known regarding how ASFV regulates the translational machinery in infected cells, although a recent report has shown a mechanism for favored expression of viral genes based on compartmentalization of viral mRNA and ribosomes with cellular translation factors within the virus factory. The viral mechanisms involved both in the regulation of host genes transcription and in the control of cellular protein synthesis are summarized in this review.

MicroRNAs, hepatitis C virus, and HCV/HIV-1 co-infection: new insights in pathogenesis and therapy

MicroRNAs (miRNAs) can exert a profound effect on Hepatitis C virus (HCV) replication. The interaction of HCV with the highly liver-enriched miRNA, miR-122 represents one such unique example of viruses having evolved mechanism(s) to usurp the host miRNA machinery to support viral life cycle. Furthermore, HCV infection can also trigger changes in the cellular miRNA profile, which may ultimately contribute to the outcome of viral infection. Accumulating knowledge on HCV-host miRNA interactions has ultimately influenced the design of therapeutic interventions against chronic HCV infection. The importance of microRNA modulation in Human Immunodeficiency Virus (HIV-1) replication has been reported, albeit only in the context of HIV-1 mono-infection. The development of HCV infection is dramatically influenced during co-infection with HIV-1. Here, we review the current knowledge on miRNAs in HCV mono-infection. In addition, we discuss the potential role of some miRNAs, identified from the analyses of public data, in HCV/HIV-1 co-infection.

COX-2 expression is upregulated by DNA hypomethylation after hematopoietic stem cell transplantation

Hematopoietic stem cell transplant therapy is limited by pulmonary infections. Mice with fully reconstituted hematopoietic compartments, including alveolar macrophages (AMs), after bone marrow transplantation (BMT) have impaired host defense against Gram-negative Pseudomonas aeruginosa. Impaired innate immunity is related to increased production of PGE(2) by AMs. Cyclooxygenase (COX)-2 is the rate-limiting enzyme for synthesis of PGE(2) from arachidonic acid, and COX-2 expression is elevated in AMs post-BMT. We hypothesized that epigenetic mechanisms may be responsible for upregulation of COX-2 in AMs. Using bisulfite sequencing, we observed the 5'-untranslated region and exon 1 of the COX-2 gene is hypomethylated in the AMs of BMT mice compared with control. COX-2 expression was increased in primary AMs and in the AM cell line (MHS) after treatment with 5-aza-2'-deoxycytidine (a methyltransferase inhibitor). Methylation by SssI methyltransferase of a 698-bp region of the COX-2 promoter including the beginning of exon 1 driving a luciferase reporter silenced luciferase expression. Because TGF-β1 is elevated in lungs post-BMT, we tested whether TGF-β1 could promote expression of COX-2 in a hypermethylated COX-2 vector, and observed TGF-β1-induced modest expression of COX-2, suggesting an ability to demethylate the promoter. Finally, BMTs performed with marrow from mice expressing a dominant-negative form of the TGF-βRII on CD11c-expressing cells (which includes AMs) demonstrated improved host defense and AM function. Our findings suggest impaired innate immunity and PGE(2) elevation post-BMT are due to hypomethylation of the COX-2 gene, which is at least partly regulated by TGF-β1.

MicroRNAs and hepatitis C virus: toward the end of miR-122 supremacy

The most common etiologic agents causing chronic hepatitis are hepatitis C and B viruses (HCV and HBV, respectively). Chronic infection caused by HCV is considered one of the major causative agents of liver cirrhosis and hepatocellular carcinoma worldwide. In combination with the increasing rate of new HCV infections, the lack of a current vaccine and/or an effective treatment for this virus continues to be a major public health challenge. The development of new treatments requires a better understanding of the virus and its interaction with the different components of the host cell. MicroRNAs (miRNAs) are small non-coding RNAs functioning as negative regulators of gene expression and represent an interesting lead to study HCV infection and to identify new therapeutic targets. Until now, microRNA-122 (miR-122) and its implication in HCV infection have been the focus of different published studies and reviews. Here we will review recent advances in the relationship between HCV infection and miRNAs, showing that some of them emerge in publications as challengers against the supremacy of miR-122.