Structural interrogation of vaccine- and infection-induced B cell responses

Immunodominance, the observation that epitopes on an antigen are not "born equal", poses a major challenge for next-generation vaccines against rapidly evolving pathogens. An underlying premise of this proposal is that in order to engage in rational immunogen design for next-generation vaccines, we first need to answer a fundamental question in immunology -- namely how to define immunodominance in biochemical and structural terms. Rather than relying on animal models that could complicate the direct translation to human health, we will directly sample both the circulating (plasmablasts and memory B cells) and tissue-resident (germinal center) B cells in humans. First, we will use structural biology approaches - primarily cryo-EM - to ask what an immunodominance map of an initial immunization looks like on a protein structure level (Aim 1). Specifically, we will establish epitopic heatmaps of antigen-specific B cells after vaccination in humans, using SARS-CoV-2 spike glycoprotein as a model antigen. Studies with other viruses like influenza have shown that pre-existing immunity generated upon primary infection biases all subsequent immune responses (to infection and to vaccination). In influenza, the issue is the immunodominance of epitopes that readily mutate (antigenic drift) and make the seasonal reformulation of the vaccine required. In our recent study of vaccination against SARS-CoV-2, we noted an original antigenic sin-like backboost to the spikes of two seasonal human coronaviruses OC43 and HKU1. Antibodies derived from the cross-reactive B cells had higher levels of mutation than did the strain-specific ones. We therefore wish to know how pre-existing immunity, generated by preceding infection, affects immunological memory and de novo responses to subsequent vaccination (Aim 2). We will follow the maturation of immune responses longitudinally. We will a) determine the somatic genetic relationships among responding B cells during primary and recall responses b) examine the resulting antibody (Ab) specificity and affinity maturation and c) follow the evolution of immunodominance heatmaps over time across B cell compartments. Recent emergence of SARS-CoV-2 variants of concern (VOCs) has made it clear that the virus mutates to avoid immune responses on a population level. However, how much antigenic variation is allowed so that there is still vaccine protection against different variants is unknown. We will concurrently follow the B responses "breakthrough infections" and sequence the infecting strain to understand the epitopic distance that permits reinfection (Aim 3). The overarching goal of this proposal is to understand the structural features of immune imprinting and, ultimately, the structural correlates of Ab protection against evolving viruses. Insights gained will not only shed light on the basic B cell biology but will also inform better vaccines. We will use SARS-CoV-2 as a model but we will extend to other coronaviruses as probes of the immune system's ability to mount an appropriate antiviral response. A particular strength of this proposal is the use of structural biology to gain atomic level, mechanistic understanding of the evolution of the Ab response with direct, single-cell interrogation of B cell responses in humans.