Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells

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

B cell responses are critical for antiviral immunity. However, a comprehensive picture of antigen-specific B cell differentiation, clonal proliferation, and dynamics in different organs after infection is lacking. Here, by combining single-cell RNA and B cell receptor (BCR) sequencing of antigen-specific cells in lymph nodes, spleen, and lungs after influenza infection in mice, we identify several germinal center (GC) B cell subpopulations and organ-specific differences that persist over the course of the response. We discover transcriptional differences between memory cells in lungs and lymphoid organs and organ-restricted clonal expansion. Remarkably, we find significant clonal overlap between GC-derived memory and plasma cells. By combining BCR-mutational analyses with monoclonal antibody (mAb) expression and affinity measurements, we find that memory B cells are highly diverse and can be selected from both low- and high-affinity precursors. By linking antigen recognition with transcriptional programming, clonal proliferation, and differentiation, these finding provide important advances in our understanding of antiviral immunity.