High-throughput specificity profiling of antibody libraries using ribosome display and microfluidics

In this work, we developed PolyMap (polyclonal mapping), a high-throughput method for mapping protein-protein interactions. We demonstrated the mapping of thousands of antigen-antibody interactions between diverse antibody libraries isolated from convalescent and vaccinated COVID-19 donors and a set of clinically relevant SARS-CoV-2 spike variants. We identified over 150 antibodies with a variety of distinctive binding patterns toward the antigen variants and found a broader binding profile, including targeting of the Omicron variant, in the antibody repertoires of more recent donors. We then used these data to select mixtures of a small number of clones with complementary reactivity that together provide strong potency and broad neutralization. PolyMap is a generalizable platform that can be used for one-pot epitope mapping, immune repertoire profiling, and therapeutic design and, in the future, could be expanded to other families of interacting proteins. [Display omitted] •PolyMap is a high-throughput platform for pairwise mapping of protein-protein interactions•PolyMap combines bulk binding to ribosome-display libraries with scRNA-seq•We demonstrate mapping of human antibody binding to SARS-CoV-2 spike variants•Mixtures of clones with distinct PolyMap profiles show improved function High-throughput methods for pairwise mapping of protein-protein interactions would enable a deeper understanding of biological processes, such as natural antibody responses; however, current techniques are limited by the number of interactions that can be screened at once. To overcome this, we have developed PolyMap (polyclonal mapping), a system based on the bulk binding of a ribosome-displayed antibody library to a library of cell-surface-expressed antigens, combined with single-cell analysis using droplet microfluidics. Wagner et al. develop PolyMap, a platform that uses ribosome display and single-cell RNA sequencing to screen antibody binding to a library of cell-surface-expressed antigens. Using this system, they map the binding of diverse human donor-derived antibodies to SARS-CoV-2 spike protein variants and further characterize unique clones.