BiGCN Learns B Cell Functional States by Integrating Single‐Cell Transcriptomes and BCR Repertoires

B lymphocytes are pivotal players in immune regulation and disease progression, yet their full functional diversity has remained elusive due to the siloed analysis of single-cell transcriptomes and B cell receptor (BCR) repertoires. Here, we present BiGCN, a novel method that explicitly integrates transcriptomic and BCR data at single-cell resolution. By uniting these two modalities within a unified embedding using a graph convolutional network (GCN) framework, BiGCN enables high-fidelity characterization of B cell states and clonal relationships. Applying BiGCN across a wide spectrum of paired single - cell RNA sequencing (scRNA-seq) and single -cell BCR sequencing (scBCR-seq) datasets, including infectious disease, autoimmunity, and a comprehensive pan-cancer atlas, we demonstrate that BiGCN markedly outperforms existing approaches in information integration, functional annotation, and biological insight. BiGCN not only recapitulates the trajectory from B cell maturation to immunoglobulin class switching but also discovers intermediate B cell subtypes and reveals functional states that are otherwise obscured by conventional analyses. Our results establish BiGCN as a versatile and robust platform for B cells research, accelerating discoveries in immunology, cancer biology, and systems medicine.