Somatic Genome Diversification and Clonal Evolution of Pathogenic B Cells in Systemic Autoimmunity

Systemic autoimmune rheumatic diseases are characterized by persistent immune activation and clinical heterogeneity, yet the molecular processes sustaining and diversifying pathogenic immune states remain incompletely understood. Here, we investigate somatic genome diversification as a potential driver of immune variation and disease progression. Using Systemic Lupus Erythematosus as a model disease, we generated a subset-resolved map of somatic mutations across B-cell subsets from 35 patients. Double-negative (DN) B cells carried the highest mutational burden, which was associated with disease duration and immunosuppressive therapy, rather than with disease activity. Integration with single-cell transcriptomes linked DN mutations to dysregulated signalling and proteostasis. Notably, DN cells harboured mutations in genes recurrently altered in B-cell lymphomas. Together, these findings identify somatic genome diversification as a feature of pathogenic B-cell subsets and provide a resource for understanding how chronic stimulation and therapeutic pressure shape the clonal evolution of autoimmunity. KEY POINTSO_LIDouble-negative B cells in SLE carry the highest somatic mutational burden among circulating B-cell subsets and show evidence of treatment-associated mutational processes. C_LIO_LIPathogenic variants in DN cells are acquired de novo or through selective expansion of pre-existing variant-bearing clones. C_LIO_LIAcquisition of lymphoma-relevant mutations by DN cells is common, supporting a molecular-level linkage between chronic systemic autoimmunity and B-cell malignancies. C_LIO_LIThe high-depth, subset-resolved map provides a foundational resource for the functional prioritization of variants and the development of targeted sequencing strategies for monitoring pathogenic clones. C_LI