Modulation of alternative splicing during early infection of human primary B lymphocytes with Epstein-Barr virus (EBV): a novel function for the viral EBNA-LP protein

Carcinogenic mechanisms of virus-associated lymphoma

The development of lymphoma is a complex multistep process that integrates numerous experimental findings and clinical data that have not yet yielded a definitive explanation. Studies of oncogenic viruses can help to deepen insight into the pathogenesis of lymphoma, and identifying associations between lymphoma and viruses that are established and unidentified should lead to cellular and pharmacologically targeted antiviral strategies for treating malignant lymphoma. This review focuses on the pathogenesis of lymphomas associated with hepatitis B and C, Epstein-Barr, and human immunodeficiency viruses as well as Kaposi sarcoma-associated herpesvirus to clarify the current status of basic information and recent advances in the development of virus-associated lymphomas.

Analysis of alternative splicing in chicken macrophages infected with avian pathogenic E. coli (APEC)

Colibacillosis is a complex disease that caused by avian pathogenic Escherichia coli (APEC), resulting in huge economic loss to the global poultry industry and threatening to human health. Alternative splicing (AS) is a universal post-transcriptional regulatory mechanism, which can simultaneously produce many proteins from a single gene to involve in various diseases and individual development. Herein, we characterized genome-wide AS events in wild type macrophages (WT) and APEC infected macrophages (APEC) by high-throughput RNA sequencing technology. A total of 751 differentially expressed (DE) AS genes were identified in the comparison of APEC vs. WT, including 587 of SE, 114 of MXE, 25 of RI, 17 of A3 and 8 of A5 event. Functional analysis showed that these identified DE AS genes were involved in 'Endocytosis', 'p53 signaling pathway', 'MAPK signaling pathway', 'NOD-like receptor signaling pathway', 'Ubiquitin mediated proteolysis' and 'Focal adhesion' immune related pathways. In summary, we comprehensively investigate AS events during APEC infection. This study has expanded our understanding of the process of APEC infection and provided new insights for further treatment options for APEC infection.

Expression and Clinical Significance of Peripheral Blood IL-17A, IL-22, Tim-3, and gal-9 in Children with Infectious Mononucleosis

To investigate the expression and clinical significance of peripheral blood interleukin (IL)-17A, IL-22, T cell immunoglobulin molecule-3 (Tim-3), and galectin-9 (gal-9) in children with infectious mononucleosis (IM) caused by the Epstein-Barr virus (EBV). Peripheral blood of 54 children with IM (case group) was collected and divided into a liver damage group and a non-liver damage group. During the same period, 20 healthy children were in the control group. IL-17A and IL-22 were measured by enzyme-linked immunosorbent assay. Real-time quantitative polymerase chain reaction was used to measure the mRNA expression of Tim-3 and gal-9. Their correlation with clinical indicators was then analyzed. The IL-17A expression level was higher in the case group than in the control group, while Tim-3, gal-9, and IL-22 were lower than those in the control group. Tim-3 was positively correlated with gal-9, but negatively correlated with IL-17A. Tim-3 and gal-9 were positively correlated with CD4+/CD8+ cells. Conversely, they were negatively correlated with CD3+, CD3+CD8+, white blood cell, lymphocyte (L), alanine transaminase (ALT), aspartate transaminase (AST), glutamyl transpeptidase (GGT), and lactate dehydrogenase (LDH). In the case group, IL-17A was positively correlated with L, GGT, and LDH, but negatively correlated with the natural killer (NK) cell count. IL-17A and IL-22 were positively correlated with CD3+, CD3+CD8+, ALT, and AST, but they were negatively correlated with the ratio of CD4+/CD8+. In the liver damage group, IL-17A, IL-22, CD3+, CD3+CD8+, immunoglobulin A (IgA), IgG, IgM, L, ALT, AST, GGT, LDH, and α-hydroxybutyrate levels were higher than those in the non-liver damage group. However, Tim-3, gal-9, the ratio of CD4+/CD8+, and NK were lower than those in the non-liver damage group. IL-17A, IL-22, Tim-3, and gal-9 are involved in the immune pathogenesis of IM caused by EBV infection in children, which may be related to immune liver injury.

EBV and Lymphomagenesis

The clinical significance of Epstein–Barr virus (EBV) cannot be understated. Not only does it infect approximately 90% of the world’s population, but it is also associated with numerous pathologies. Diseases linked to this virus include hematologic malignancies such as diffuse large B-cell lymphoma, Hodgkin lymphoma, Burkitt lymphoma, primary CNS lymphoma, and NK/T-cell lymphoma, epithelial malignancies such as nasopharyngeal carcinoma and gastric cancer, autoimmune diseases such as multiple sclerosis, Graves’ disease, and lupus. While treatment for these disease states is ever evolving, much work remains to more fully elucidate the relationship between EBV, its associated disease states, and their treatments. This paper begins with an overview of EBV latency and latency-associated proteins. It will then review EBV’s contributions to select hematologic malignancies with a focus on the contribution of latent proteins as well as their associated management.

All differential on the splicing front: Host alternative splicing alters the landscape of virus-host conflict

Alternative RNA splicing is a co-transcriptional process that richly increases proteome diversity, and is dynamically regulated based on cell species, lineage, and activation state. Virus infection in vertebrate hosts results in rapid host transcriptome-wide changes, and regulation of alternative splicing can direct a combinatorial effect on the host transcriptome. There has been a recent increase in genome-wide studies evaluating host alternative splicing during viral infection, which integrates well with prior knowledge on viral interactions with host splicing proteins. A critical challenge remains in linking how these individual events direct global changes, and whether alternative splicing is an overall favorable pathway for fending off or supporting viral infection. Here, we introduce the process of alternative splicing, discuss how to analyze splice regulation, and detail studies on genome-wide and splice factor changes during viral infection. We seek to highlight where the field can focus on moving forward, and how incorporation of a virus-host co-evolutionary perspective can benefit this burgeoning subject.

Reversal of splicing infidelity is a pre-activation step in B cell differentiation

Introduction

B cell activation and differentiation is central to the adaptive immune response. Changes in exon usage can have major impacts on cellular signaling and differentiation but have not been systematically explored in differentiating B cells.

Methods

We analyzed exon usage and intron retention in RNA-Seq data from subsets of human B cells at various stages of differentiation, and in an in vitro laboratory model of B cell activation and differentiation (Epstein Barr virus infection).

Results

Blood naïve B cells were found to have an unusual splicing profile, with unannotated splicing events in over 30% of expressed genes. Splicing changed substantially upon naïve B cell entry into secondary lymphoid tissue and before activation, involving significant increases in exon commitment and reductions in intron retention. These changes preferentially involved short introns with weak splice sites and were likely mediated by an overall increase in splicing efficiency induced by the lymphoid environment. The majority of transcripts affected by splicing changes showed restoration of encoded conserved protein domains and/or reduced targeting to the nonsense-mediated decay pathway. Affected genes were enriched in functionally important immune cell activation pathways such as antigen-mediated signaling, cell cycle control and mRNA processing and splicing.

Discussion

Functional observations from donor B cell subsets in progressive states of differentiation and from timecourse experiments using the in vitro model suggest that these widespread changes in mRNA splicing play a role in preparing naïve B cells for the decisive step of antigen-mediated activation and differentiation.

Tumor Molecular and Microenvironment Characteristics in EBV-Associated Malignancies as Potential Therapeutic Targets: Focus on Gastric Cancer

Although most people are infected with Epstein-Barr Virus (EBV) during their lifetime, only a minority of them develop an EBV-associated malignancy. EBV acts in both direct and indirect ways to transform infected cells into tumor cells. There are multiple ways in which the EBV, host, and tumor environment interact to promote malignant transformation. This paper focuses on some of the mechanisms that EBV uses to transform the tumor microenvironment (TME) of EBV-associated gastric cancer (EBVaGC) for its benefit, including overexpression of Indoleamine 2,3-Dioxygenase 1 (IDO1), synergism between H. pylori and EBV co-infection, and M1 to M2 switch. In this review, we expand on different modalities and combinatorial approaches to therapeutically target this mechanism.

Role of Epitranscriptomic and Epigenetic Modifications during the Lytic and Latent Phases of Herpesvirus Infections

Herpesviruses are double-stranded DNA viruses occurring at a high prevalence in the human population and are responsible for a wide array of clinical manifestations and diseases, from mild to severe. These viruses are classified in three subfamilies (Alpha-, Beta- and Gammaherpesvirinae), with eight members currently known to infect humans. Importantly, all herpesviruses can establish lifelong latent infections with symptomatic or asymptomatic lytic reactivations. Accumulating evidence suggest that chemical modifications of viral RNA and DNA during the lytic and latent phases of the infections caused by these viruses, are likely to play relevant roles in key aspects of the life cycle of these viruses by modulating and regulating their replication, establishment of latency and evasion of the host antiviral response. Here, we review and discuss current evidence regarding epitranscriptomic and epigenetic modifications of herpesviruses and how these can influence their life cycles. While epitranscriptomic modifications such as m⁶A are the most studied to date and relate to positive effects over the replication of herpesviruses, epigenetic modifications of the viral genome are generally associated with defense mechanisms of the host cells to suppress viral gene transcription. However, herpesviruses can modulate these modifications to their own benefit to persist in the host, undergo latency and sporadically reactivate.

Impaired surface marker expression in stimulated Epstein-Barr virus transformed lymphoblasts from Barth Syndrome patients

Primary B lymphocytes rapidly respond to lipopolysaccharide (LPS) and cytosine linked to a guanine by a phosphate bond deoxyribonucleic acid (CpG DNA) stimulation to promote adaptive immune function through increased surface marker expression. Here we examined expression of surface markers in LPS and CpG DNA stimulated Epstein-Barr virus transformed B lymphoblasts from control and BTHS patients with different mutations. The percentage of cluster of differentiation (CD) positive cells including CD38 + , CD138 + , CD80 + surface expression and programmed cell death protein 1 (PD1 +) surface expression was similar between control and BTHS lymphoblasts incubated plus or minus LPS. The percentage of CD24 + , CD38 + and CD138 + cells was similar between control and BTHS lymphoblasts incubated plus or minus CpG DNA. CD27 + surface marker expression was reduced in both BTHS lymphoblasts and controls incubated with CpG DNA and PD1 + surface marker expression was higher in BTHS cells compared to controls but was unaltered by CpG DNA treatment. Thus, Epstein-Barr virus transformed control and BTHS lymphoblasts fail to increase selected surface markers upon stimulation with LPS and exhibit variable surface marker expression upon stimulation with CpG DNA. Since B lymphocyte surface marker expression upon activation is involved in B cell proliferation and differentiation, cell-cell interaction and the adaptive immune response, we suggest that caution should be exercised when interpreting immunological data obtained from Epstein-Barr virus transformed BTHS cells. Based upon our observations in control cells, our conclusions may be more broadly applicable to other diseases which utilize transformed B lymphocytes for the study of immune biology.