Deconvolution of B-cell heterogeneity identifies PDIA6 as a prognostic driver in hepatocellular carcinoma

Background B cells are integral components of the tumor microenvironment (TME) and play a pivotal role in regulating anti-tumor immunity. However, the systematic classification of B-cell-associated molecular features in hepatocellular carcinoma (HCC) and their value in clinical prognosis and immunotherapy remain elusive. Methods We elucidated the molecular characteristics of B cells within the HCC TME based on single-cell RNA sequencing (scRNA-seq) data and constructed B-cell-associated molecular subtypes by integrating bulk RNA sequencing data. We systematically evaluated differences across subtypes regarding clinical prognosis, biological processes, genomic variations, the immune microenvironment, and immunotherapeutic responses. Furthermore, a B-cell-associated gene signature score (BCAGS) prognostic model was established using 117 combinations of machine learning algorithms. Finally, key genes were selected for in vitro functional validation. Results Based on B cell marker genes, we identified three molecular subtypes with significantly distinct clinical outcomes, validating their robustness across multiple external cohorts. The C2 subtype exhibited higher genomic instability and the poorest prognosis, whereas the C3 subtype presented an "immune-hot" phenotype with predicted sensitivity to immunotherapy. Additionally, the BCAGS was confirmed as an independent risk factor for HCC patients, demonstrating superior predictive performance compared to existing models. Functional experiments further revealed that silencing the key gene, PDIA6 , significantly inhibited the proliferation, migration, and invasion of HCC cells. Conclusions This study systematically unveils the heterogeneity of B-cell-associated molecular subtypes in HCC and their clinical significance, establishing a robust BCAGS prognostic model. Combined with in vitro validation, the results suggest that PDIA6 may play a critical role in promoting HCC progression, providing a novel theoretical basis for precision stratification and the development of potential therapeutic targets in HCC.