Unveiling the dynamics of B lymphocytes in systemic lupus erythematosus patients treated with belimumab through longitudinal single-cell RNA sequencing

Abstract Objectives Unravelling the mechanisms underlying treatment response for targeted therapeutics in systemic lupus erythematosus (SLE) patients is challenging due to the limited understanding of diverse responses of circulating immune cells, particularly B cells. We investigated B lymphocyte dynamics during anti-BAFF treatment, utilizing longitudinal single-cell transcriptome data. Methods We conducted single-cell RNA sequencing on peripheral blood mononuclear cells (PBMCs) in four Korean SLE patients before and after belimumab treatment at the following time points: 2 weeks, 1, 3, 6 and 12 months. Results Analysing over 73 000 PBMCs, we identified eight distinct subsets of B cells and plasmablasts and analysed dynamic changes within these cell subsets: initial declines in naïve and transitional B cells followed by an increase at 3 months, contrasted by an initial increase and subsequent decrease in memory B cells by the third month. Meanwhile, plasmablasts exhibited a consistent decline throughout the treatment. B cell activation pathways, specifically in naïve and memory B cells, were downregulated during the third and sixth months. These findings were validated at the protein level throughout the first 4 weeks of treatment using flow cytometry. Comparative analysis with bulk transcriptome data from 22 Japanese SLE patients showed increased NR4A1 expression 6 months post-belimumab treatment, indicating its role in restricting self-reactive B cells, thereby contributing to the biological responses of anti-BAFF treatment. Conclusion The observed B cell dynamics provided insights into the immunological mechanisms underlying the therapeutic effects of anti-BAFF in SLE patients. Furthermore, it underscores the need for research in predicting drug responses based on immune profiling.