Single-cell multi-omics reveals circulating B cell heterogeneity across diverse disease contexts

B cells play essential roles in adaptive immunity by producing antigen-specific antibodies and interacting with T cells. Single-cell RNA and BCR sequencing technologies have enabled high-resolution dissection of B cell heterogeneity across diverse disease contexts. Atypical B cells (ABCs) display complex and critical functions in human immunity, yet their transcriptional heterogeneity, BCR diversity, and context-specific roles remain incompletely understood.

In this study, we performed an integrative reanalysis of public single-cell RNA sequencing and single-cell B cell receptor (BCR) sequencing data derived from human peripheral blood mononuclear cells (PBMCs) across four distinct clinical contexts, including systemic lupus erythematosus (SLE), immunotherapy-treated melanoma, human immunodeficiency virus (HIV) blip, and age-stratified influenza vaccination. We established a unified analytical framework integrating transcriptomic profiling, BCR embedding-based clustering, and connectivity analysis to systematically characterize circulating B cell transcriptional features, BCR connectivity, and the correlation between transcriptomic and BCR diversity.

Our analysis revealed substantial dynamics in B cell transcriptomics and BCR repertoires across diverse time points and conditions. Notably, ABCs exhibited dynamic fluctuations, strong activation and BCR signaling, and marked transcriptomic diversity in response to autoreactive antigens, immunotherapy, transient viremia, and vaccination, positioning them as critical mediators of B cell responses. By integrating ABCs across all conditions, we identified nine distinct ABC clusters exhibiting specific transcriptional signatures associated with chemotaxis, complement activation, T cell regulation, plasma cell differentiation, or progenitor-like states. These ABC clusters displayed either phenotype-specific or shared distribution patterns, along with varying degrees of B cell activation, BCR signaling, and BCR connectivity across different phenotypes, suggesting divergent functional roles of ABCs.

Collectively, our cross-context analysis provides a broad characterization of circulating B cell heterogeneity, BCR diversity, and their associations in diverse conditions, advancing the understanding of ABC functional roles in human diseases. These findings highlight the potential of ABCs as key modulators of B cell responses across autoimmune, cancer, infection, and vaccine contexts.