Core D: Antibodyomics Core

University Of California Berkeley, Berkeley CA

Investigators

Linked publications & trials

Abstract

SUMMARY (CORE D) Dengue is caused by four mosquito-borne flaviviruses (DENV1-4), with an estimated 100 million symptomatic infections per year. Antibodies (Abs) elicited to one DENV serotype can protect against or enhance subsequent infection with a heterologous serotype to cause severe disease, due in part to antibody-dependent enhancement. For this reason, development of safe, effective dengue vaccines has been particularly challenging. The complexities of DENV Ab responses highlight the necessity of comprehensive profiling of the identity, abundance, and functionality of circulating Abs elicited by DENV infection and vaccination. The Antibodyomics Core (Core D) employs two innovative pipelines, Ig-seq and BCR-seq, which together can comprehensively determine, at high throughput, both the B cell and serological mAb repertoires elicited by DENV infection or vaccination. Working with Projects 1 and 2, and Cores B and C, Core D will comprehensively profile serum and peripheral blood mononuclear cell samples from robust, well-established cohorts across the P01, including the ongoing 20- year Pediatric Dengue Cohort Study and Pediatric Hospital-based Dengue Study in Nicaragua, a Philippine cohort of children vaccinated with Dengvaxia, and a NIH monovalent DENV3 vaccine challenge study. The tools developed by Core D are a synergistic combination of Ab mass spectrometry, bulk B cell receptor sequencing, and a single B cell sequencing method that preserves natural VH:VL pairs and facilitates identification and testing of DENV-specific recombinant Abs mined directly from serum. This approach will be the first of its kind—an integrative B cell and secreted Ab repertoire analysis—in 1° and 2° DENV infection or vaccination, revealing the immune repertoire of responding B cells and the Abs that they secrete. Aim 1 examines the serum Ab epitope landscape after 1° infection (with Project 1 and Core B) to establish baseline differences in envelope (E) epitope targeting between serotypes. We hypothesize that 1° infection of each DENV serotype results in a distinct epitope profile of both neutralizing and non-neutralizing Abs within the circulating IgG repertoire. Aim 2 seeks to define how the serotype-dependent Ab imprint acquired after 1° infection or vaccination (with Project 1, Project 2, Core B, and Core C) impacts 2° serum Ab responses, in relation to specific 1°/2° serotype sequences of infection or antigenic distances. Lastly, Aim 3 seeks to correlate the serological Ab epitope landscape and serum Ab features, such as Ab subclass, glycosylation status, and Fc effector function, with functional outcomes by examining serotype-matched sample sets of non-severe versus severe dengue (with Project 1 and Core B). In summary, Core D will enable comprehensive, high-resolution proteomic profiling of the identity, abundance, epitope specificity, and functionality of circulating Abs at monoclonal resolution to help elucidate imprinting in sequential DENV infections and unravel the complex interplay between protective and disease-enhancing serum Ab responses triggered by 1° and 2° DENV infections or vaccination.