Single cell BCR and transcriptome analysis after respiratory virus infection reveals spatiotemporal dynamics of antigen-specific B cell responses

Mathew, Nimitha R.; Jayanthan, Jayalal K.; Smirnov, Ilya; Robinson, Jonathan L.; Axelsson, Hannes; Nakka, Sravya S.; Emmanouilidi, Aikaterini; Czarnewski, Paulo; Yewdell, William T.; Lebrero-Fernández, Cristina; Bernasconi, Valentina; Harandi, Ali M.; Lycke, Nils; Borcherding, Nicholas; Yewdell, Jonathan W.; Greiff, Victor; Bemark, Mats; Angeletti, Davide

B cell responses are a critical component of anti-viral immunity. However, a comprehensive picture of antigen-specific B cell responses, differentiation, clonal proliferation and dynamics in different organs after infection is lacking. Here, we combined single-cell RNA sequencing with single-cell B cell receptor (BCR) characterization of antigen-specific cells in the draining lymph nodes, spleen and lungs after influenza infection. We identify several novel B cell subpopulations forming after infection and find organ-specific differences that persist over the course of the response. We discover important transcriptional differences between memory cells in lungs and lymphoid organs and describe organ-restricted clonal expansion. Strikingly, by combining BCR mutational analysis, monoclonal antibody expression and affinity measurements we find no differences between germinal center (GC)-derived memory and plasmacells, at odds with an affinity-based selection model. By linking antigen-recognition with transcriptional programming, clonal-proliferation and differentiation, these finding provide important advances in our understanding of antiviral B cell immunity.