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

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.