Date of Award

Fall 2022

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Immunobiology

First Advisor

Iwasaki, Akiko

Abstract

Respiratory viruses represent a continuous and growing threat to humanity. This is exemplified by the ongoing global COVID-19 pandemic, which is caused by a newly emerged coronavirus SARS-CoV-2. The immune system provides a formidable barrier to viral pathogens, while dysregulated immunity leads to deleterious infection outcomes. Understanding the involvement of immune responses in viral infections will provide crucial insights into disease pathogenesis and shed light on potential targets for therapeutic interventions. In this thesis, we interrogate the components of the immune response that control SARS-CoV-2 and contribute to its pathogenesis. Based on these insights, we develop distinct immunopharmacological strategies to strengthen protection against viral infection, disease, and transmission. In chapter 2, we investigated the prevalence, magnitude, and specificity of autoantibody (AAb) responses against the human exoproteome in SARS-CoV-2-infected individuals using a high-throughput AAb discovery technology called Rapid Extracellular Antigen Profiling (REAP). Infection with SARS-CoV-2 leads to diverse immunological and clinical outcomes. However, the impact of AAbs on these infection outcomes remains unknown. We found that patients with COVID-19 exhibit increases in autoreactivities against a broad array of immunological antigens, including cytokines, chemokines, and cell surface proteins. We uncovered mechanisms by which AAbs interfere with immunological functions, by perturbing immunoreceptor signaling, by depleting circulating leukocytes, and by dampening antiviral antibody responses. Murine AAb surrogates similarly hinder immune activation and exacerbate disease in a mouse model of SARS-CoV-2. Collectively, through the lens of an unbiased proteome-scale discovery campaign for AAbs, these findings implicate humoral immunopathology as an integral aspect of COVID-19 pathogenesis with diverse impacts on immune functionality and clinical outcomes. In chapter 3, we developed a therapeutic strategy that bolsters type I interferon (IFN-I)-dependent innate immunity against SARS-CoV-2 on the basis of a synthetic RNA ligand of RIG-I, stem-loop RNA 14 (SLR14). The IFN system presents a critical protective barrier against viral pathogens but is also capable of contributing to pathogenesis. Our discovery in chapter 2 that preexisting IFN-I-neutralizing AAbs are associated with poor disease prognosis in patients with COVID-19 suggests a protective role for IFN-I. We discovered that a single dose of SLR14 confers robust antiviral protection in mouse models of SARS-CoV-2 infection by eliciting systemic and mucosal IFN-I responses. SLR14 is the most protective when administered prophylactically or early after viral exposure. We further demonstrated that SLR14 elicits sterilizing immunity in immunodeficient mice chronically infected with SARS-CoV-2 independent of the adaptive immune system and confers broad-spectrum protection against emerging variants of concerns (VOCs). This study demonstrates the potential of leveraging host-directed nucleic acid therapeutics to induce protective antiviral immunity against SARS-CoV-2. In chapter 4, we developed a novel vaccine strategy, Prime and Spike, that elicits mucosal immunity against SARS-CoV-2. Parenteral vaccines induce robust systemic immunity, but poor immunity at the respiratory mucosa. We designed a vaccination regimen that converts existing circulating immunological effector mechanisms generated by primary vaccination (Prime) into mucosal immunity in the respiratory tract via unadjuvanted intranasal (IN) spike boosting (Spike). We established that Prime and Spike induces tissue-resident memory T cells and B cells, promotes mucosal IgA, boosts systemic immunity, protects mice with waning immunity from lethal disease, and reduces viral shedding in a hamster model of contact transmission. We demonstrated IN spike boosters can be delivered in the format of unadjuvanted recombinant spike proteins or spike-encoding mRNA encapsulated by immunosilent poly(amine-co-ester) (PACE) polymers. Using divergent spike proteins, we showed that Prime and Spike enables the induction of cross-reactive immunity against sarbecoviruses. These findings suggest that Prime and Spike can be exploited as a potent prophylactic vaccine platform to elicit pan-sarbecovirus mucosal immunity. In chapter 5, we employed a different, but just as devasting disease model to study factors governing the induction of protective immunity. In the context of melanoma, we identified type 1 conventional dendritic cells (cDC1s) as a crucial innate immunological determinant for effective anti-PD-1 (αPD-1) cancer immunotherapy. While cDC1s critically mediate the initiation of anti-tumor CD8+ T cell immunity, whether they contribute to effector CD8+ T cells during αPD-1 therapy remains unclear. We discovered that cDC1s enables αPD-1 therapy by unleashing the terminal differentiation and expansion of intratumoral CD8 T cells at the effector phase of αPD-1 therapy. We found that tumor cDC1 abundance predicts strong tumor infiltration by CD8+ T cells and associates with clinical responses to αPD-1 treatment in human cancer patients. Together, this study suggests that the development of efficacious cancer immunotherapeutics should incorporate strategies that engage cDC1 immunity. In conclusion, the collective work presented in this thesis addresses both discovery and application-oriented research questions, provides important insights into the role of immune system in the control of infection and tumorigenesis, and expands the therapeutic toolkit for tackling human viral diseases and malignancies.

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