Browsing by Subject "Interferon"

The intracellular innate immune response to viral infection is among the first lines of defense against these pathogens. For the early establishment of an antiviral cellular state and initiation of inflammatory responses, type I interferons (IFNs) are particularly important, as they potently induce the production of hundreds of IFN-stimulated genes (ISGs), many of which have antiviral functions. The type I IFN response requires tight molecular coordination to achieve both efficient production of antiviral proteins and controlled shutoff of inflammatory responses to avoid tissue damage and autoimmunity. Despite the importance of regulation of this antiviral response, current knowledge of the molecular controls governing its activation and suppression remains incomplete. Further, although ISGs have diverse functions and are induced to differing potencies, our understanding of regulatory controls governing the expression of individual or subclasses of ISGs is limited. Current knowledge of type I IFN response regulation is predominantly centered on transcriptional and post-translational regulatory controls. However, post-transcriptional regulation of antiviral responses has begun to emerge as an important layer of control. An example of these post-transcriptional regulatory controls is the RNA base modification N6-methyladenosine (m6A), which regulates many aspects of mRNA metabolism through transcript-specific effects. m6A deposition is mediated by a cellular complex of proteins including METTL3 and METTL14 (METTL3/14) and other cofactors, and m6A can also be removed from RNA by the demethylase proteins FTO and ALKBH5. The presence of m6A on viral and host RNAs has been shown to influence the outcome of infection by diverse viruses. However, the role of m6A in the response to type I IFNs has not been explored. To investigate the role of m6A in the type I IFN response, we began by manipulating m6A levels in the transcriptome through perturbation of the expression of the cellular m6A machinery and measuring the induction of ISGs after IFN treatment. We found that depletion of the m6A methyltransferase proteins METTL3 and METTL14 (METTL3/14) resulted in less protein production of a subset of ISGs, including the antiviral genes IFITM1 and MX1, after IFN treatment. However, the expression of other ISGs and the overall activation of the IFN responses were unchanged. Using methyl RNA immunoprecipitation and sequencing (meRIP-seq), we found that the transcripts of many ISGs are modified by m6A, and these included the METTL3/14-regulated ISGs IFITM1 and MX1 that we had identified. Using polysome profiling and ribosome profiling, we determined that METTL3/14-regulated ISGs are translationally enhanced by METTL3/14. Additionally, ablation of putative m6A sites within the 3’UTR of IFITM1 decreased the translation of a reporter molecule. Overexpression of the m6A reader protein YTHDF1, which has known roles in promoting translation, enhanced the expression of IFITM1 in an m6A binding-dependent fashion. These experiments characterized METTL3/14 and m6A as novel enhancers of the type I IFN response. To determine whether m6A contributes to type I IFN-mediated viral restriction, we depleted or overexpressed METTL3/14 and pretreated cells with a low dose of IFN-β prior to infection with vesicular stomatitis virus (VSV). Interestingly, METTL3/14 depletion decreased the expression of ISGs and allowed increased VSV infection, while METTL3/14 overexpression had the opposite effect. Together, these studies demonstrate that METTL3/14 and m6A enhance the antiviral effect of type I IFN by promoting the translation of ISGs to support the establishment of an antiviral cellular state. Having discovered a role for m6A in the type I IFN response, we also investigated the role of an m6A demethylase protein, FTO. FTO polymorphisms can have profound effects on human health. Certain polymorphisms are associated with fat mass and obesity, cardiovascular disease, while others can cause growth retardation or embryonic lethality. However, the molecular functions of FTO and the cellular pathways that it affects are still not well characterized. We depleted FTO and measured the production of ISGs following IFN-β treatment and found that the production of m6A-regulated ISGs was increased, as expected. However, unexpectedly, we found that FTO depletion increased the mRNA levels of a subset of ISGs. Pulse labeling of nascent transcripts revealed that FTO suppresses the transcription of these ISGs and that FTO-depleted cells are primed for the production of certain ISGs in response to IFN. We then used cells lacking PCIF1, the writer of 2’-O-N6-dimethyladenosine (m6Am), an RNA modification that FTO can also remove, and found that FTO-mediated regulation of ISGs occurs independently of the m6Am modification. These results identify FTO as a transcriptional regulator of a subset of ISGs, which will add an important dimension to our understanding of the molecular functions of FTO and its contributions to inflammatory disease. Future research revealing the mechanisms by which FTO suppresses ISG transcription will be of great interest. Together, these data identify novel functions of m6A and its related cellular machinery in both positive and negative regulation of the type I IFN response and antiviral gene expression.

In the 21st century, the world has already experienced two pandemics caused by respiratory RNA viruses, the 2009 H1N1 “swine-flu” pandemic, and the ongoing COVID-19 pandemic. The 2009 pandemic was, thankfully, mild in terms of casualties; however, it revealed certain failings in existing systems. As a circulating virus, we had approved, in-use antiviral treatments for influenza, but the 2009 H1N1 viruses were resistant to an entire class, adamantanes. Also, the requirement for annually updated influenza vaccines meant there were systems in place for large-scale vaccine production, yet reliance on eggs dramatically limited the ability to scale-up a new vaccine quickly. Finally, global vaccine inequities meant many countries remained relatively unvaccinated against the H1N1 virus, even as the pandemic was declared over in August 2010. The COVID-19 pandemic has been a very different story on some fronts, most notably the death toll, which exceeds 6 million globally. Also, the decade of progress in vaccine research since 2009 has been evident in the rapid development of many highly effective COVID-19 vaccines using different platforms, while vaccine distribution issues remain. Finally, an entire lack of approved coronavirus antivirals required swift action to identify existing drugs and treatments to alleviate disease. The research and clinical response to the COVID-19 pandemic took advantage of existing technologies, pharmaceuticals, and systems and adapted them to solve the present crisis. The problem of this dissertation is to extend these efforts by investing in adaptable research tools, methods, and subjects to prepare for potential future respiratory RNA virus pandemics.In Chapters 2 and 3, we generated virus-specific research tools that are rapidly adaptable to new viral strains. Chapter 2 describes a fluorescent reporter of coronavirus protease activity that may be used to screen antiviral drugs and is compatible with diverse coronavirus protease proteins. Chapter 3 discusses a novel method for generating influenza reporter viruses with wide research applications, notably this manner of introducing exogenous proteins requires minimal genome rearrangements increasing transferability to newly identified strains. These projects demonstrate that even research tools requiring updates with the emergence of new strains can be designed to prioritize rapid adaptability. In Chapters 4 and 5, we interrogate the innate immune responses that determine the outcomes of viral infections. Chapter 4 identifies ETV7 as a negative regulator of the antiviral type I interferon response using CRISPR activation screening. ETV7 was previously known to be induced by interferon, but its role during the response to viral infection remained undetermined. We found ETV7 limits transcription of interferon stimulated gene expression, influencing the antiviral state of a responding cell. Chapter 5 reviews the impact of influenza viral disease outside the site of infection, the respiratory tract, and established methods of studying these effects using animal models. Many of the circulating cytokines implicated in non-respiratory influenza disease from these models, IL-6, IFNs, and TNF-alpha, are known to play a role in influenza and COVID-19 patient disease severity. These investigations show that our understanding of how innate immunity is regulated, and dysregulated, continues to require updating even as the main pathway members and downstream effectors have been identified.

Malignant glioma formation involves an abundant inflammatory infiltrate dominated by glioma-associated macrophages and microglia (GAMM). GAMM constitutes a large portion of the glioma mass and tumor microenvironment. They are actively involved in tissue repair and immune surveillance, however in the tumor microenvironment (TME), they are subverted to promote tumor progression. The human poliovirus receptor, hCD155h, is constitutively expressed in members of the mononuclear phagocytic system and is upregulated ectopically in the neoplastic compartment of malignant gliomas (and solid cancers in general). Intratumor treatment with the highly attenuated rhino:poliovirus chimera, PVSRIPO, has a dual effect of releasing neoantigens by oncolysis and activating the GAMM component via sublethal infection, leading to a substantial but transient immune therapy effect. In a phase I clinical trial, PVSRIPO treatment resulted in 21% long-term survival with durable radiographic responses in patients with recurrent glioblastoma (Desjardins et al. New England Journal of Medicine, 2018). Therefore, studying the mechanisms of PVSRIPO immunotherapy in mouse brain tumor models to decipher contributions of viral infection to GAMM vs. malignant cells is critical to improving the therapeutic efficacy in ongoing clinical trials. We recapitulated the clinical trial scenario in an immunocompetent intracerebral mouse tumor model (CT2A-CD155) and obtained baseline and post treatment brain in a time series. Histopathology studies, combined with detailed multiplex IHC/IF and RNAseq were performed on tumor bearing brains. We found the PVSRIPO therapy induced intense engagement of the GAMM infiltrate accompanied by substantial, but transient tumor regression. There were extensive microglia activation and proliferation in adjacent brain parenchyma and even part of the contralateral cortex. This occurred against a backdrop of sustained innate antiviral inflammation and is associated with an induction of the PD-L1 immune checkpoint on GAMM. In contrast to transient antitumor effects observed after PVSRIPO monotherapy, combining PVSRIPO with PD1/PD-L1 blockade led to durable remission. Our work implicates GAMM as active drivers of inflammation and reveals broad neuroinflammatory activation of the CNS-resident myeloid compartment upon polio virotherapy of malignant glioma.

The Immunity-Related GTPases (IRGs) are a family of dynamin-like proteins found in vertebrates that play critical roles in cell-autonomous resistance to bacteria and protozoa. The IRGs are divided into two subfamilies, with the GMS IRGs exerting a regulatory function over the GKS IRGs, affecting GKS IRG expression, localization, and ultimately function. The profound loss of host resistance seen in mice lacking the GMS protein Irgm1 suggests that GMS IRGs may additionally have broader functions beyond the regulation of GKS IRGs, though the nature of these functions remains poorly understood. In this dissertation, we address the regulatory functions of GMS IRGs in mouse cells.

We first addressed regulation of GKS IRGs (Irga6 and Irgb6) by GMS IRGs (Irgm1 and Irgm3). We found that in both fibroblasts and macrophages lacking these GMS IRGs, that the GKS IRGs relocalized to form punctate structures that were ubiquitin-, p62-, and LC3-positive. A biochemical analysis indicated that the GKS IRGs were directly ubiquitinated through K63 linkages. Collectively, these results suggested that GMS IRGs regulate aggregation of GKS IRGs and their transfer to autophagosomes through one of at least two possible mechanisms -- by the direct association of GMS IRGs with GKS IRGs to block their aggregation that subsequently leads to autophagic removal, and/or by directly promoting autophagic removal of spontaneously forming GKS aggregates. The latter hypothesis was addressed using a series of complementary assays, which ultimately showed that absence of Irgm1 has no effect on the maturation of autophagosomes in fibroblasts, and only a very small and statistically insignificant effect in macrophages. Thus, we conclude that the major mechanism through which GMS IRGs regulate GKS IRGs is by directly inhibiting their aggregation, rather than through general effects on autophagic initiation or maturation of GKS IRG-containing autophagosomes.

We also addressed the possibility of broad regulatory functions of GMS IRGs beyond the regulation of GKS IRGs by examining whether GMS IRGs can affect another family of dynamin-like GTPases, the guanylate-binding proteins (GBPs). Despite no previous evidence of interactions between these two protein families, we found that the absence of GMS IRGs had striking effects on the localization of the murine Gbp2, leading it to colocalize with GKS IRG aggregates formed as a consequence of GMS IRG deficiency. We further demonstrated that unlike the GKS IRGs, Gbp2 was not tagged with K63-linked ubiquitin chains, which might have targeted it for specific macroautophagy, implying that Gbp2 is not aggregating in the absence of Irgm1. We then showed both that Gbp2 forms puncta in the presence of generic protein aggregates, and that guanylate-binding proteins including Gbp2 promote the degradation of GKS IRG protein aggregates. These findings suggest that GMS IRGs do not exert direct control over GBPs, but rather that GBPs are involved in the macroautophagic degradation of protein aggregates as a primary function, and are thus influenced indirectly by GMS IRGs.

In total, our experiments contribute to the understanding of regulatory interactions among GMS IRGs, GKS IRGs, and GBPs. These results will be important in establishing the mechanisms through which these important families of proteins influence eradication of bacterial and protozoan pathogens through key innate immune mechanisms.

Vaccinia virus (VV) is the most thoroughly studied member of the Poxviridae family and the vaccine used to achieve the only successful eradication of a human disease. Over the years, it has proven itself as a useful tool for the study of antiviral immunity, vaccine development, and potentially cancer immunotherapy. VV is capable of eliciting a robust immune response; however the mechanisms by which VV accomplishes this task remain unknown. The overall goal of this thesis project is to determine how VV activates the innate immune system, and how this activation contributes to viral clearance in vivo. We determined that VV or VV-DNA activated the TLR8-MyD88 pathway in plasmacytoid dendritic cells (pDC), resulting in the production of type I interferons (IFN). We also demonstrated that TLR8-mediated production of type I IFN by pDC was crucial to efficient VV control and clearance in vivo. Moreover, we identified the polyA- and polyT-rich sequences in VV-DNA was the possible motif recognize by TLR8. Type I IFN, known for ability to establish the "antiviral state", are also critical mediators of NK cell activation. In the setting of VV infection, we demonstrated that direct action of type I IFN on NK cells, but not accessory cells such as DC, was necessary for NK cell activation in vivo. We further demonstrated that type I IFN-dependent activation of NK cells was required for optimal VV clearance in vivo. Given the importance of NK cells in anti-VV innate immunity, we next examined what role the TLR2-MyD88 pathway, critical for activation of cDC, played in the activation of NK cells. NK cells from TLR2-/- or MyD88-/- mice displayed a reduction in activation and cytolytic function, and this defect was independent of pro-inflammatory cytokine signaling. We were able to demonstrate that direct TLR2 signaling on NK cells was required for their optimal activation and function in response to VV infection. Moreover, we were able to demonstrate that TLR2-MyD88 signaling resulted in the activation of the PI3K-ERK pathway, which was necessary for NK cell cytotoxicity. In addition, we identified the NKG2D pathway as critical for efficient NK cell activation and function in response to VV infection, independent of the TLR2 pathway. Both the NKG2D and TLR2 pathways were crucial for optimal VV clearance and control in vivo. Collectively, this project illuminates the roles and mechanisms of the innate immune system in the control of VV in vivo.

The IFN-γ/STAT1 response is an immune signaling pathway well known for its potent pro-inflammatory and anti-viral functions. However, IFN-γ/STAT1 signaling also impacts many homeostatic and pathological aspects in the central nervous system, beyond its canonical role in controlling intracellular pathogens. IFN-γ can modulate neuronal excitability, synaptic pruning, and gene expression of pathways associated with neurodevelopmental disorders, including autism spectrum disorder (ASD) and schizophrenia (SZ). Surprisingly, the IFN response was recently identified as the most highly enriched pathway in brains of individuals with ASD and SZ. Children born to mothers who are hospitalized for infection during pregnancy are at a higher risk of developing ASD, and mouse models demonstrate that elevating cytokines during embryonic neurodevelopment cause ASD-like phenotypes. While microglia are thought to be the major targets of IFNs in the brain, neurons can respond to IFNs and require physiological levels of IFN-γ for proper function. The IFN-γ/STAT1 pathway is rapidly activated then deactivated to prevent excessive inflammation; however, neurons utilize unique IFN-γ/STAT1 activation patterns, which may contribute to the non-canonical neuron-specific downstream effects. We hypothesized that pathological IFN-γ signaling in neurons leads to neuronal dysfunction and behavioral deficits through non-canonical STAT1 signaling. Using primary neuron cultures, we demonstrated that developing neurons have differential STAT1 activation downstream of physiological versus pathological IFN-γ. Physiological levels of IFN-γ caused brief and transient STAT1 activation, while high pathological levels of IFN-γ caused robust and prolonged activation of STAT1 in neurons, but not in microglia or astrocytes. To determine the effects of prolonged STAT1 activation in vivo, we developed a novel mouse model in which STAT1 signaling is prolonged in neurons. These mice displayed hyperactive behavior and neural hypoactivity, which are common comorbidities of neurodevelopmental disorders like ASD and attention deficit hyperactivity disorder (ADHD). Moreover, we demonstrated that this phenotype is neuron specific, as mice with prolonged STAT1 activation in microglia did not have behavior deficits. Our findings suggest pathological activation of the IFN-γ/STAT1 pathway contributes to neuronal dysfunction through non-canonical STAT1 activation. Overall, the IFN-γ/STAT1 pathway is critical for normal neurodevelopment and neuronal function in adulthood and provides new insight into a neuron specific neuroimmune mechanism which may contribute to the pathophysiology of neurodevelopmental disorders.