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Bats asymptomatically host a number of viruses that are the cause of recently emergent infectious diseases in humans. While the mechanisms underlying this asymptomatic infection are currently not known, studies of sequenced bat genomes help uncover genetic adaptations in bats that may have functional importance in the antiviral response of these animals. To identify differences between antiviral mechanisms in humans and bats, we sequenced, assembled, and analyzed the genome of the Egyptian rousette bat (ERB; Rousettus aegyptiacus), a natural reservoir of Marburg virus and the only known reservoir for any filovirus. We used this genome to understand the evolution of immune genes and gene families in bats, and describe several observations relevant to defense against viruses. We observed an unusual expansion of the NKG2/CD94 natural killer (NK) cell receptor gene families in Egyptian rousette bats relative to other species, and found genomic evidence of unique features and expression of these receptors that may result in a net inhibitory balance within bat NK cells. The expansion of NK cell receptors is matched by an expansion of potential major histocompatibility complex (MHC) class I ligands, which are distributed both within and, surprisingly, outside the canonical MHC loci. We also observed that the type I interferon (IFN) locus is considerably expanded and diversified in the ERB, and that the IFN-ω subfamily contributes most to this expansion. To understand the functional implications of this expansion, we synthesized multiple IFN-ω proteins and examined their antiviral effects. Members of this subfamily are not constitutively expressed but are induced after viral infection, and show antiviral activity in vitro, with different antiviral potencies observed for different IFN-ω proteins. Taken together, these results show that multiple bats, including the ERB, have expanded and diversified numerous antiviral loci, and potentially developed unique adaptations in NK cell receptor signaling, and type I IFN responses. The concerted evolution of so many key components of immunity in the ERB is strongly suggestive of novel modes of antiviral defense that may contribute to the ability of bats to asymptomatically host viruses that are pathogenic in humans.

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Infectious diseases are the leading cause of illness worldwide, leading to over 20 million hospitalizations each year in the United States alone. Although numerous diseases are treatable with vaccines and pharmacological agents, including antibiotics, a large fraction of infections remain poorly controlled, mainly due to lack of effective therapies and/or vaccines. Two such infectious agents are influenza A virus and the bacterium Salmonella enterica. Influenza A virus is transmitted through the aerosol route and infects lung epithelial cells, while Salmonella is transmitted via the fecal-oral route and infects the cells lining the intestine of the host. In each case, the first lines of defense against these infectious agents are non-phagocytic cells. How these pathogens are controlled in non-phagocytic cells dictates the overall outcome of infection; however there are significant gaps in our knowledge of how non-phagocytic cells respond to influenza A virus and Salmonella. Therefore, studying the fate of these cells during the course of infection is of crucial importance to disease outcome. In each case, the regulated (or programmed) death of the infected cell may represent an important pathogen clearance mechanism. Programmed cell death can be non-inflammatory (e.g., apoptosis) or pro-inflammatory (e.g., necroptosis and pyroptosis). In this dissertation, I outline experiments carried out to identify the pathways of programmed cell death activated by Salmonella and influenza A virus in their respective target non-phagocytic cells, both in vitro and in vivo. My work outlines new pathways of cell death activated by these pathogens and new mechanisms of both viral and bacterial clearance. This will have broad implications in the clearance of pathogens, and new therapeutic avenues to pursue upon treating infections. / Biomedical Sciences

Signal Transducer and Activator of Transcription (STAT) 2 is one of seven members of the STAT family of transcription factors with dual roles in signal transduction and gene activation. STAT2 is a central transcription factor that regulates the antiviral, apoptotic and cell growth inhibitory effects of type I interferons (IFN-α/β), a small family of secreted glycoproteins induced by the host after sensing the presence of tumor cells and pathogens. The creation of Stat2-/- mice established the pivotal role of STAT2 in type I IFN signaling and in antiviral immunity. In vitro studies conducted in STAT2 deficient tumor cell lines suggested a role in suppressing tumor cell growth in response to IFN treatment. Based on these properties STAT2 is presumed to have tumor suppressor functions but data to support this notion in animal models of cancer are limited. To address the role of STAT2 in cancer, I used the murine B16-F1 tumor transplantation model of human melanoma. The B16-F1 melanoma cell line was established from a spontaneous tumor that arose in mice. I discovered that tumor cells transplanted subcutaneously in Stat2-/- mice grew more aggressively than in the counterpart wild type mice. Closer examination of B16-F1 tumors harvested from wild type and Stat2-/- mice revealed an unexpected dramatic similar reduction of STAT2 and STAT1 proteins. Yet soluble factors secreted by B16-F1 tumors established in Stat2-/- mice alone were sufficient to enhance proliferation of B16-F1 tumor cells. I further showed that tumor-bearing wild type mice treated with IFN-β developed smaller tumors compared to Stat2-/- mice, whose tumors continued to grow and hence were unresponsive to IFN intervention. Lastly, to elucidate a mechanism that leads to enhanced tumor growth in Stat2-/- mice, I questioned the involvement of the host immune response in restricting tumor growth. I found that tumor specific T cell priming by Stat2-/- dendritic cells (DCs) was defective since generated cytotoxic T cells (CD8+ T lymphocytes) produced low levels of IFN-γ and IL-2 and adoptive transfer of these B16-F1 tumor specific CD8+ T cells in B16-F1 bearing Stat2-/- mice did not cause tumor regression with IFN-β intervention. Collectively, my findings reveal that host STAT2 restricts the establishment of melanoma tumors. More importantly, type I IFN/STAT2 signaling on DCs plays a pivotal role in tumor antigen cross-presentation to CD8+ T cells and in the development of a protective antitumor response resulting in tumor rejection. To now address whether STAT2 expression in cancer cells could influence tumor establishment and the antitumor effects of type I IFNs, STAT2 expression was silenced in B16-F1 tumor cells. Contrary to my expectation, silencing STAT2 augmented the growth inhibitory effects of IFN-β both in vitro and in vivo. However, loss of STAT2 expression in the tumor did not cause B16-F1 tumor cells to grow more aggressively compared to control B16-F1 cells. Furthermore, compared to B16-F1 control cells, STAT2-silenced B16-F1 cells showed an initial delay but later persistent STAT activation and formation of the ISGF3 transcriptional complex (consisting of STAT1, STAT2 and IRF9). This observation paralleled with an initial delay and then later an increase in the expression of IFN regulated genes. In addition, reduced activation of STAT5 induced by IFN-β was observed in STAT2-silenced B16-F1 cells. This may partially explain the enhanced growth inhibitory effects of type I IFNs. Together these results shed light on the unexpected role of tumor STAT2 expression in diminishing the efficacy of type I IFN treatment of melanoma. / Biochemistry

Innate antiviral defence depends on virus recognition and cytokines like interferon (IFN) that upregulate many interferon-stimulated genes (ISGs). Virus recognition normally relies on pattern recognition receptors binding to virus-associated nucleic acid motifs, but virus activity may provide an additional means for the cell to recognize infection. Enveloped viruses fuse with a cell membrane during entry and membrane fusion by virus-like particles or the purified protein p14 are sufficient to upregulate ISGs in the absence of viral nucleic acid. This thesis examines the mechanism by which cells recognize membrane fusion and how this affects downstream signalling and upregulation of ISGs. We found that membrane perturbation by enveloped virus particles or p14 triggered cytosolic Ca2+ oscillations important for antiviral defence. Surprisingly, Ca2+ signalling seemed to act upstream of nucleic acid sensing pathways during enveloped virus infection. In the absence of viral nucleic acid, p14 triggered a Ca2+-dependent antiviral response to dsRNA. It is still unclear how p14 might trigger recognition of endogenous dsRNA. We found that enveloped virus particles trigger IRF3-mediated upregulation of interferon as well as direct IFN-independent upregulation of ISGs. Furthermore, while some viruses like HCMV trigger widespread IRF3 activation, other viruses like SeV upregulate IRF3 and IFN in a minority of infected cells. This disparate response to infection can lead to different biological outcomes when measured at the population level. Our work highlights the complexity of the response to enveloped virus particles, despite the absence of replication. Further work is necessary to understand how membrane perturbation is recognized and how this interfaces with nucleic acid sensing. While nucleic acid sensing is sufficient to upregulate antiviral ISGs, other signals like membrane perturbation may provide important contextual cues during infection. This will be important to understand moving forward as virus-like particles are used more and more for research and clinical applications. / Thesis / Doctor of Philosophy (PhD) / Cells rely on pattern recognition receptors for innate antiviral defence. While the study of pattern recognition has focused on virus-associated nucleic acid motifs, disruptions of the cellular environment during virus infection could similarly warn the cell. Membrane perturbation during enveloped virus entry is associated with upregulation of antiviral interferon-stimulated genes. This thesis examines the mechanism of membrane perturbation sensing and different antiviral signalling pathways activated by non-replicating enveloped virus particles. We found evidence that membrane perturbation triggers cytosolic Ca2+ signalling which may act as a co-stimulatory signal for recognition of incoming viral nucleic acid. We initially thought enveloped virus particles were recognized through a common pathway, but have since learned that recognition is more complex. Further work is necessary to understand how membrane perturbation and nucleic acid sensing interface during enveloped virus infection and what role this plays in antiviral defence.