Targeting autoreactive B cells in rheumatoid arthritis through MHC class I-presented BCR-derived neo-epitopes

Somatic mutations can generate neoantigens recognized by CD8⁺ T cells, enabling targeted elimination of mutated cells. Currently established B cell-targeting therapies in human B cell-mediated autoimmune diseases lack specificity and fail to achieve durable remission. Since autoreactive B cells often express B cell receptors (BCRs) that have undergone extensive somatic hypermutations (SHM), we hypothesized that mutated BCR-derived neoantigens could be exploited to selectively target these autoreactive B cells. However, the identification, validation, and extent to which autoreactive BCR-derived neoepitopes are presented and immunogenic remains poorly understood. Here, we investigated the immunological targetability of autoreactive B cells producing anti-citrullinated protein antibodies (ACPAs) - the hallmark antibody response in rheumatoid arthritis (RA). By using an integrated approach combining in silico MHC class I binding analysis, peptide-elution mass spectrometry, and CD8⁺ T cell-activation assays, we studied 9 common HLA class I alleles and 150-patient derived BCRs. Our results predict that all autoreactive BCRs harbor sequences presentable by at least 3 HLA class I alleles. Notably, 85% of these sequences contain SHMs that introduce amino-acid changes compatible with candidate neoepitopes. Mass spectrometric analysis of HLA class I-eluted peptides from three BCR-transduced cell lines confirmed the presence of multiple predicted neoepitopes and revealed additional unpredicted, BCR-derived peptides. Importantly, several of these neoepitopes were endogenously processed, presented, and recognized by primary human CD8⁺ T cells, while their unmutated counterparts were not recognized by the same CD8⁺ T cell clones. These findings highlight that an integrative strategy, combining MHC isolation, peptide identification, and BCR sequencing, serves as a powerful platform for uncovering neoantigens presented by autoreactive B cells in a major human autoimmune disease. Likewise, they reveal a novel approach for the specific targeting of autoreactive B cells, paving the way for personalized immunotherapeutic interventions in RA and potentially other B cell-driven autoimmune diseases.