Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics

Abstract

Protective humoral memory forms in secondary lymphoid organs where B cells undergo affinity maturation and differentiation into memory or plasma cells. Here, we provide a comprehensive roadmap of human B cell maturation with single-cell transcriptomics matched with bulk and single-cell antibody repertoires to define gene expression, antibody repertoires, and clonal sharing of B cell states at single-cell resolution, including memory B cell heterogeneity that reflects diverse functional and signaling states. We reconstruct gene expression dynamics during B cell activation to reveal a pre–germinal center state primed to undergo class switch recombination and dissect how antibody class–dependent gene expression in germinal center and memory B cells is linked with a distinct transcriptional wiring with potential to influence their fate and function. Our analyses reveal the dynamic cellular states that shape human B cell–mediated immunity and highlight how antibody isotype may play a role during their antibody-based selection.

Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci

“…We also found a small and unexpected cluster of B cells expressing markers of type I interferon response genes such as IFI44L, XAF1, and MX1 (Fig1f-g) that are known to be up-regulated after early stages of vaccination (9). These annotations broadly agreed with recent single-cell studies of lymphocytes in pediatric tonsils and adult lymph node (10,11).…”

“…Other scRNA-seq analyses have recently demonstrated that tonsils are a transferable model tissue to study secondary lymphoid organs and adaptive immune responses more generally (10, 11, 16). In contrast to circulating or bone-marrow resident lymphocyte populations, immune cells within secondary lymphoid organs exist in a range of activation and maturation states, including GC-associated populations, that may reflect varied tissue niches, cell-cell communication and cytokine signaling.…”

“…We identified a secondary B cell activation state, after an initial NFκB-associated activation presumably linked with strong BCR activation and/or T cell help (45). One particularly interesting candidate for future study will be BHLHE40, which has previously been shown to be required for the transition from an activated state prior to entry into the GC (46–48) and is capable of binding key regulatory elements at the immunoglobulin heavy chain locus (10). How this, and other putative regulators we identify in this secondary activation state (such as CEBPE/Z, ZBTB33, and ZHX1) may contribute to the transition from the activated B cell state to a GC-associated gene expression program will be an important question for future mechanistic studies.…”

“…Cells were cryopreserved in 90% fetal bovine serum, 10% DMSO until use. Four additional cryopreserved tonsil samples at Queen Mary University of London included for scATAC-seq analyses were prepared as described previously (10) under approval from North West/Greater Manchester East Research Ethics Committee (17/NW/0664).…”

Compartments and Connections Within the Germinal Center

“…This study resolved a critical question in the field placing CSR in the early events during GC initiation, and validated earlier evidence that CSR might occur prior to mature GCs (33,34). The transcriptional states associated with CSR have now been resolved at the single cell level, further accelerating our understanding of early events in the GC reaction (35).…”