Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen specificity
Andreas Agrafiotis, Daniel Neumeier, Kai‐Lin Hong, Tasnia Chowdhury, Roy A. Ehling, Raphael Kuhn, Ioana Sandu, Victor Kreiner, Tudor‐Stefan Cotet, Danielle Shlesinger, Daria Laslo, Stine Anzböck, Dale Starkie, Daniel Lightwood, Annette Oxenius, Sai T. Reddy, Alexander Yermanos
Abstract
Although new genomics-based pipelines have potential to augment antibody discovery, these methods remain in their infancy due to an incomplete understanding of the selection process that governs B cell clonal selection, expansion, and antigen specificity. Furthermore, it remains unknown how factors such as aging and reduction of tolerance influence B cell selection. Here we perform single-cell sequencing of antibody repertoires and transcriptomes of murine B cells following immunizations with a model therapeutic antigen target. We determine the relationship between antibody repertoires, gene expression signatures, and antigen specificity across 100,000 B cells. Recombinant expression and characterization of 227 monoclonal antibodies revealed the existence of clonally expanded and class-switched antigen-specific B cells that were more frequent in young mice. Although integrating multiple repertoire features such as germline gene usage and transcriptional signatures failed to distinguish antigen-specific from nonspecific B cells, other features such as immunoglobulin G (IgG) subtype and sequence composition correlated with antigen specificity.