Bovine viral diarrhea virus (BVDV) is a pestivirus that suppresses the innate and adaptive host immune responses. Each of the two classified genotypes (BVDV1 and BVDV2) has two distinct biotypes – cytopathic (cp) and non-cytopathic (ncp) – and evidence has suggested that cytopathic strains may disrupt host interferon (IFN) synthesis and IFN-mediated responses. However, inconsistent results examining ncpBVDV strains have generated controversy regarding whether they also exhibit this capability. The purpose for this study was to determine the occurrence and functionality of IFN-induced responses within the serum cattle infected with ncpBVDV2-1373. Specifically, this involved analysing the changes in both the serum levels of IFN-α and IFN-γ and the expression of genes that are classically regulated by these cytokines. Serum analysis showed that the infected cattle induced both serum IFN-α and IFN-γ during BVDV infection while PBMC analysis showed increased expression of genes that classically respond to IFN-α – Mx-1, OAS-1, and STAT-1 – and IFN-γ – SOCS-1 and SOCS-3. These findings are supported by temporal kinome analysis, which verified activation of the JAK-STAT signalling network within the PBMCs of the virus-infected animals. In addition to establishing evidence for its synthesis, results from this challenge identified IFN-γ as a possible indicator of animal mortality as analysis of its change within the non-surviving, infected animals was statistically greater than the levels of the surviving, infected animals. Collectively, these results demonstrate 1373-mediated induction of, and host cell response to, both IFN-α and IFN–γ, and the potential for IFN-γ to be a predictive marker for mortality during BVDV infection.

Interferon gamma (IFN-γ) regulation of macrophages plays an essential role in innate immunity and pathogenicity of viral infections by directing large and small genome-wide changes in the transcriptional program of macrophages. Smaller changes at the transcriptional level are difficult to detect but can have profound biological effects, motivating the hypothesis of this thesis that responses of macrophages to immune activation by IFN-γ include small quantitative changes that are masked by noise but represent meaningful transcriptional systems in pathways against infection. To test this hypothesis, statistical meta-analysis of microarray studies is investigated as a tool to obtain the necessary increase in analysis sensitivity. Three meta-analysis models (Effect size model, Rank Product model, Fisher’s sum of logs) and three further modified versions were applied to a heterogeneous set of four microarray studies on the effect of IFN-γ on murine macrophages. Performance assessments include recovery of known biology and are followed by development of novel biological hypotheses through secondary analysis of meta-analysis outcomes in context of independent biological data sources. A separate network analysis of a microarray time course study investigate s if gene sets with coordinated time-dependent relationships overlap can also identify subtle IFN-γ related transcriptional changes in macrophages that match those identified through meta-analysis. It was found that all meta-analysis models can identify biologically meaningful transcription at enhanced sensitivity levels, with slightly improved performance advantages for a non-parametric model (Rank Product meta-analysis). Meta-analysis yielded consistently regulated genes, hidden in individual microarray studies, related to sterol biosynthesis (Stard3, Pgrmc1, Galnt6, Rab11a, Golga4, Lrp10), implicated in cross-talk between type II and type I interferon or IL-10 signalling (Tbk1, Ikbke, Clic4, Ptpre, Batf), and circadian rhythm (Csnk1e). Further network analysis confirms that meta-analysis findings are highly concentrated in a distinct immune response cluster of co-expressed genes, and also identifies global expression modularisation in IFN-γ treated macrophages, pointing to Trafd1 as a central anti-correlated node topologically linked to interactions with down-regulated sterol biosynthesis pathway members. Outcomes from this thesis suggest that small transcriptional changes in IFN-γ activated macrophages can be detected by enhancing sensitivity through combination of multiple microarray studies. Together with use of bioinformatical resources, independent data sets and network analysis, further validation assigns a potential role for low or variable transcription genes in linking type II interferon signalling to type I and TLR signalling, as well as the sterol metabolic network.

Recently, cholesterol metabolism has been shown to modulate the infection of several viruses and there is growing evidence that inflammatory response to infection also modulates lipid metabolism. However little is known about the role of inflammatory processes in modulating lipid metabolism and their consequences for the viral infection. This study investigates host-lipid viral interaction pathways using mouse cytomegalovirus, a large double-stranded DNA genome, which represents one of the few models for a natural infection of its natural host. In this study, transcriptomic and lipidomic profiling of macrophages shows that there is a specific coordinated regulation of the sterol pathways upon viral infection or treatment with IFNγ or β (but not TNFα, IL1β or IL6) resulting in the decrease of free cellular cholesterol. Furthermore, we show that pharmacological and RNAi inhibition of the sterol pathway augments protection against infection in vitro and in vivo and we identified that the prenylation branch of the sterol metabolic network was involved in the protective response. Finally, we show that genetic knock out of IFNβ results in a partial reduction while genetic knock out of Ifnar1 completely abolishes the reduction of the sterol biosynthetic activity upon infection. Overall these results support a role for part of the sterol metabolic network in protective immunity and show that type 1 IFN signalling is both necessary and sufficient for reducing the sterol metabolic network upon infection; thereby linking the sterol pathway with IFN defence responses.

Interferon (IFN) and phosphatidylinositol 3-kinase (PI3K) are apoptosis regulators that are targeted by viruses to promote survival of infected cells. Significant crosstalk exists between IFN and PI3K, and this study sought to investigate the relationships between IFN, PI3K and apoptosis during virus infection. Parainfluenza virus 5 (PIV5) and influenza A virus (IAV) are both negative-sense single-stranded RNA viruses that encode multifunctional proteins in order to maximise their genome coding capacity. The PIV5 V and IAV NS1 proteins are well-studied as IFN antagonists and, in addition, both are reported to modulate PI3K signalling. Less well-studied is the role of these proteins in apoptosis regulation; the ability of V and NS1 to inhibit apoptosis was therefore investigated. PIV5/V was found to limit cell death in response to a number of apoptosis inducers in a manner that required its STAT1- degradative activity and also inhibited activation of the PI3K downstream target, Akt. IAV/NS1 binds directly to PI3K to stimulate its activity, and this is reported to mediate anti-apoptotic signalling during IAV infection. However, a virus expressing an NS1 unable to bind PI3K did not induce more apoptosis than wt virus. NS1 expression, either in a stable cell-line or during virus infection, was also unable to protect cells from pro-apoptotic stimuli. NS1-mediated PI3K activation similarly had no effect on IFN production or ISG expression in infected cells. In contrast, other NS1 mutant viruses induced large amounts of apoptosis. These viruses also induced significant levels of IFN and were unable to cause apoptosis in IFN-deficient cells, indicating that NS1 limits apoptosis induction through its IFN antagonist functions. The implications of this work for anti-cancer and anti-viral therapies are discussed.

published_or_final_version / abstract / Paediatrics and Adolescent Medicine / Master / Master of Philosophy

The transcription factor Interferon Regulatory Factor-1 (IRF-1) has been demonstrated to suppress tumour growth through the regulation of many anti-oncogenic genes. Pro- and anti-apoptotic factors, cell cycle control genes, DNA damage response genes and prometastatic factors are all under the control of IRF-1, which effects both transcriptional activation and repression. In addition to these cell autonomous tumour suppressor activities, IRF-1 is also a key regulator of the immune system and, as such, mediates immune surveillance of tumours. Numerous studies have confirmed that loss or mis-regulation of IRF-1 is a key factor in several different types of cancer. Despite strong evidence for the crucial role of IRF-1 in cancer, and frequent assertions that this protein warrants further investigation as a drug target, very little is known about its regulation. Furthermore, since recent studies have linked upregulation of IRF-1 to the development of autoimmune diseases, it is particularly important that drugs be able to decouple autoimmune and anti-cancer functions of IRF-1 to avoid harmful side effects. This thesis describes how phosphorylation of IRF-1 in its regulatory C-terminal Mf1 domain modulates transactivatory and tumour suppressor activity. Phosphospecific antibodies were developed as tools to study the C-terminal phosphorylation. Using these, it was shown that treatment of cells with Interferon-γ(IFN-γ) not only causes accumulation of IRF-1 protein, but also results in phosphorylation of IRF-1 at two sites in the C-terminal Mf1 domain. Phosphomimetic mutants demonstrated that these phosphorylations enhanced the transactivatory activity of IRF-1 at various promoters, but did not affect repressor activity. Gel shift assays revealed that dual phosphorylation of IRF-1 (IRF-1 D/D) promoted DNAbinding and suggested this was through increased interaction with the cofactor/histone acetylase p300 which induces a conformational change in IRF-1, favouring DNA-binding. Acetylation by p300 appears to be important although it is not yet clear whether this directly or indirectly affects IRF-1 activity. Since the tumour suppressor activity of IRF-1 is of particular interest, the effect of phosphorylation was examined in clonogenic and invasion assays. IRF-1 D/D more efficiently suppressed colony formation in both anchorage dependent and independent assays, and may improve inhibition of invasion in Transwell assays. Thus, cell treatment with the therapeutic agent IFN-γ nduces phosphorylation of IRF-1, resulting in enhanced DNA binding of IRF-1 through improved p300 binding. In cells the outcome is more effective tumour suppression and inhibition of metastasis.

A Thesis submitted to The University of Arizona College of Medicine - Phoenix in partial fulfillment of the requirements for the Degree of Doctor of Medicine. / In this study we examine the utility of using CD8+ T cell hybridomas to measure the ability of bone marrow dendritic cells (BMDCs) to internalize cancer proteins and display them to cytotoxic T cells, a process termed cross‐presentation. We test the ability of a newly generated T cell hybridoma called BUSA14 to detect cross‐presentation of the melanoma antigen gp100. BUSA14 produces a dose‐dependent response to human and mouse gp100 peptides. However, cross‐presentation of gp100 by BMDCs using SK‐MEL‐28 human melanoma cell lysates or direct MHC class I‐restricted presentation by B16 murine melanoma cells was not detected. Both SKMEL‐28 and B16 cells express gp100 protein by immunoblot, and gp100 as a membrane bound protein may be concentrated by cell fractionation techniques. We validated our crosspresentation assay with another T cell hybridoma B3Z to detect cross‐presentation of the model antigen ovalbumin. Lastly, we determined that although BUSA14 expresses the coreceptor CD8, BUSA14 lacks CD3 expression, which likely impairs the ability of this hybridoma to respond to engagement of the T cell receptor and contributes to the inability to detect presentation of native gp100 protein. To resolve these issues, we plan to use primary gp100‐specific T cells from pmel mice expressing the same T cell receptor as the BUSA14 hybridoma to detect presentation of gp100 protein. Ultimately, we plan to evaluate the requirements for cross‐presentation of gp100, including a role for gamma‐interferon‐inducible lysosomal thiol reductase (GILT), a disulfide bond reducing enzyme.

Mast cells respond to a variety of signals, are associated with both increased inflammation and regulation of the immune response, and are able to interact with a variety of hematopoietic and non-hematopoietic cells. The majority of the work that highlights mast cell pleiotropic abilities has been completed in murine models. Though these models have significantly advanced our understanding of what mast cells can do, they cannot inform us as to what mast cells actually do in human beings. The goal of this dissertation is to assess fully mature, primary human mast cell function beyond the well-defined type 1 hypersensitivity function and place mature human mast cells in the context of interactions with other immune cells. The first project addresses the ability of IFNγ, a historically Th1 associated cytokine, to dramatically alter mast cell phenotype. In particular, IFNγ stimulation allows mast cells to act as antigen presenting cells to CD4+ T cells. The second project describes and addresses the T cell suppressive function of myeloid derived suppressor cells in Mastocytosis, a disease of clonal mast cells.

Interferon γ is an important T-cell helper type 1 (Th1) cytokine involves in antimicrobial immunity. It is a part of the inflammatory immune response in the site of infection. However, for its proper function, the regulation of immunity is necessary to avoid injury of the tissue caused by long-term inflammation. While interferon γ triggers expression of proinflammatory genes, it also regulates genes which inactivate immune response. The B7-H1 molecule belongs among these inhibitory regulators. Furthermore, antitumour effect of interferon γ is well-known as well. After extensive experiments, interferon γ was tested as an immunotherapeutic drug against melanomas in clinical trials. However, the trials had to be terminated prematurely because of unsuccessful results. It started to be clear that interferon γ could have also a protumour effect. Interferon γ upregulates the expression of B7-H1 molecule which aids tumour in escape from immunity. The B7-H1 molecule possesses a binding site for interferon regulatory factor 1 (IRF-1) in its promoter region. This IRF-1 is induced by interferon γ - JAK/STAT signalling pathway. In our previous research, we observed interferon γ induced DNA demethylation of promoters in genes that are involved in antigen presenting machinery. Additionally, DNA methylation of...

Multiple Sklerose (MS) ist eine chronisch-entzündliche Erkrankung des Zentralen Nervensystems mit deutlich ausgeprägten Autoimmunphänomenen. Das derzeit meistverwendete Therapeutikum zur Sekundärprophylaxe von Krankheitsschüben ist rekombinantes Interferon-β (IFN-β). Wirk- und Nebenwirkungsmechanismen des Medikaments werden bisher nur partiell verstanden. In der Pathogenese der MS spielt eine Familie chemotaktisch wirksamer Zytokine, der Chemokine, eine entscheidende Rolle. Ziel dieser Studie war zu untersuchen, ob IFN-β die systemischen Konzentrationen der Pathogenese-relevanten Chemokine CXCL10, CCL2 und außerdem des endogenen Pyrogens IL-6 verändert, und ob diese Veränderungen mit dem Auftreten grippeartiger Nebenwirkungen korrelieren. Zu diesem Zweck wurden bei 37 Patienten mit schubförmiger MS zu drei Zeitpunkten – vor sowie 6 und 24 Stunden nach der Applikation von IFN-β – die genannten Botenstoffe im Blut bestimmt. Parallel wurden subjektiv empfundene grippeartige Nebenwirkungen mit Hilfe eines standardisierten Fragebogens abgefragt, und die Körperkerntemperatur wurde gemessen. Als Kontrollen dienten gesunde Probanden, derzeit nicht immunmodulatorisch behandelte MS-Patienten und MS-Patienten unter Therapie mit Glatirameracetat. Nur bei den mit IFN-β behandelten Patienten zeigte sich nach 6 Stunden ein signifikanter transienter Anstieg der Konzentrationen von CXCL10, CCL2. Der Anstieg der Chemokinkonzentrationen korrelierte mit einem transienten IL-6-Anstieg und dem Auftreten grippeartiger Nebenwirkungen. Chemokine, unter denen sich zahlreiche starke endogene Pyrogene befinden, könnten somit für die häufig zu beobachtenden grippeartigen Nebenwirkungen mit verantwortlich sein. Die Ergebnisse werfen die weiterführende Frage auf, ob die beobachtete Chemokininduktion auch relevant für den therapeutischen Effekt von IFN- ist. Ob Chemokine sich erfolgreich als Biomarker zur Prädiktion des Therapieerfolgs einsetzen lassen, wird derzeit in einem weiterführenden Projekt untersucht. / Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system with clear autoimmune phenomena. Recombinant Interferon-β (IFN-β) is currently the most widely used treatment to prevent relapses. The mechanisms and side effects of the drug are only partially understood. A family of chemotactical active cytokines, the chemokines, play a decisive role in the pathogenesis of MS. The aim of this study was to examine if IFN-β alters the systemic concentrations of CXCL10 and CCL2, two chemokines that are relevant in the pathogenesis, and of IL-6, an endogenous pyrogen. A further aim was to discover whether these concentrations correlate with the appearance of flu-like symptoms, a common adverse effect of IFN-β. 37 patients with relapsing-remitting MS were tested three times to measure the chemokine concentrations in their blood – prior to IFN-β application, and again 6 and 24 hours after application. Concurrently, the occurrence of flu-like symptoms was recorded with the help of a standardized questionnaire and through body temperature measurements. The control groups consisted of healthy subjects, MS patients not receiving any treatment, and MS patients treated with glatiramer acetate. After 6 hours, only the MS patients treated with IFN-β showed a significant transient elevation in the concentrations of CXCL10 and CCL2. This elevation correlated with a transient increase in the IL-6 concentration and the appearance of flu-like symptoms. Among the chemokines there are many strong endogenous pyrogens, which might be responsible for the commonly observed, flu-like side effects of IFN-β. The results raise the question of whether the observed induction of chemokines is also relevant for the therapeutic effect of IFN-β. Whether chemokines can be used as biomarkers to predict therapeutic success is currently being explored in ongoing work built upon this study.