Single-cell analysis reveals multi-faceted features of B cell development, together with age-associated B cell subpopulations

The development and maturation of B lymphocytes are critical for adaptive immunity, relying on tightly regulated gene programs within specialized microenvironments shaped by extracellular matrix and neighboring cells. However, high-dimensional, integrated analyses of B cell heterogeneity, gene regulation, and external factors during development remain limited. Here, we analyze single-cell transcriptomic and B cell receptor (BCR) sequencing data from B cells and surrounding cells in bone marrow, tonsil, and peripheral blood. We reveal the dynamics of gene regulation, the heterogeneity of conventional B cells, and stage-specific cell-cell interactions along B cell development. Immature B cells display minimal transcriptional activity and low RNA velocity, whereas naïve B cell proliferation and activation are niche-confined and individualized. Two models for memory B cell subpopulation development appear compatible and warrant further study. Cell-cell interaction analysis highlights the role of myeloid cells and identifies TNF and adhesion signaling as dominant, stage-dependent pathways. Additionally, we identify two age-associated B cell subpopulations expressing S100A8/A9 and C1q, and experimentally confirm S100A8/A9 secretion from human B cells, indicating a senescence-associated secretory phenotype. This integrated analysis provides a comprehensive resource for understanding B cell development, gene regulation, and intercellular communication, offering insights into immune aging and potential therapeutic strategies.