Single–amino acid variants in target epitopes can confer resistance to antibody-based therapies

Monoclonal antibodies have transformed the therapeutic landscape across oncology, immunology, and infectious diseases by enabling high-affinity, antigen-specific targeting to neutralize soluble molecules, block cellular interactions, or deplete cells. Although high specificity is critical for safety, it may confer an inherent susceptibility to even minor variations in the target epitope. Here, we investigated the impact of natural single-nucleotide variants on antigen recognition by therapeutic monoclonal antibodies, both approved and in clinical development. For almost every antibody analyzed, we identified protein variants in or near the antibody-antigen interface, a subset of which were predicted to disrupt antigen recognition. Experimental studies corroborated the impact of select variants for four different antigens, revealing complete loss of antibody binding in some cases. For example, a human breast cancer cell line overexpressing human epidermal growth factor receptor 2 (HER-2), but engineered to carry the HER-2^P594H variant, was completely resistant to killing even by highly potent clinical antibody-drug conjugates. These findings suggest that natural variants can confer primary resistance to antibody-based therapies, with critical implications for treatment outcomes, patient management, and safety, particularly in the context of potent modalities such as antibody-drug conjugates. Individual resistance-associated variants, although globally rare, are enriched in specific populations, underscoring the importance of accounting for genetic diversity in both drug development and clinical decision-making.