Discovery and Characterization of Next-Generation Antibody and Vaccine Candidates

Abstract

Vaccines represent one of the most successful medical interventions in history, and their efficacy is dependent on the induction of a robust and long-lasting immune response, classically through the elicitation of neutralizing antibodies. Traditional immunization strategies have utilized live-attenuated or inactivated versions of the pathogen; however, this approach has fallen short of generating effective vaccines against modern emerging, and highly mutable pathogens. Modern strategies instead aim to identify protective epitopes and correlates of immunity from natural infection or vaccination models to inform the rational design of immunogens that elicit sterilizing immunity. Here, we applied advancements in high-throughput antibody discovery, and next-generation sequencing towards the rational design of protective vaccines or antibody therapeutics against Human Immunodeficiency Virus (HIV-1), Hepatitis C Virus (HCV), and Staphylococcus aureus. First, we profiled the antibody specificities elicited by chronic HIV-1/HCV co-infection using LIBRA-seq, a technology that leverages DNA-barcoded antigens to enable simultaneous recovery of B cell receptor sequence and specificity by next-generation sequencing. We discovered the first natural bispecific HIV-1/HCV cross-reactive antibodies and characterized their epitope specificity and development using several approaches. Notably, these antibodies are cross-functional, broadly neutralizing against HCV, and could have the potential to aid cross-reactive vaccine design or serve as therapeutics themselves for both HIV-1 and HCV. Next, we describe the design and testing of a multi-subunit Staphyloccocus aureus vaccine that targets nutrient metal acquisition. We found that immunization with antigens targeting iron, zinc, and manganese acquisition induce superior S. aureus killing over mock-immunized controls, even when complement was inactivated. Finally, we examined how simultaneous immunization with multiple diverse immunogens affects the development of antigen-specific IgG antibody responses using pathogen-derived antigens. We discovered that although cocktail-immunized mice initially elicited more robust antibody responses, the rate of titer development decreases significantly over time compared to single antigen-immunized mice. Together, these studies aim to contribute to the development of successful vaccines against previously indomitable pathogens.