Single‐Cell Level Characterization of B Cell Depletion and Repopulation Following Rituximab in Systemic Lupus Erythematosus

OBJECTIVE: B cell depletion therapy, is frequently used to treat systemic lupus erythematosus (SLE). However, variability in patient response highlights the need for a deeper understanding of the underlying immune cell dynamics of B cell depletion and repopulation. METHODS: We conducted longitudinal single-cell profiling of nine patients with SLE treated with rituximab from pretreatment to up to 15 months post-treatment. These were compared with eight healthy controls. We profiled 169,513 immune cells via single-cell RNA, surface protein, B cell receptor (BCR), and T cell receptor sequencing, and bulk BCR repertoire sequencing. RESULTS: Significant depletion of naïve, memory, and age-associated B cells was observed early post-treatment, followed by later repopulation of mainly transitional B cells. A fraction of antigen-experienced B cells, particularly in nonresponders, persisted through the depletion. BCR repertoire analysis revealed reduced diversity and persistent clones in antigen-experienced cells at early post-treatment, but these effects were not long-lasting. Repopulated naïve B cells in rituximab responders exhibited reduced NF-κB pathway activation, aligning with lower B cell activating factor receptor (BAFF-R) surface protein levels. In non-B cells, we identified 27 differentially expressed genes across seven immune cell subtypes post-rituximab, with regulatory CD4 T cells and double negative (DN) T cells showing the most changes. Responders specifically had increased expression of genes related to cytotoxicity, major histocompatibility complex class II antigen presentation, and T cell activation in CD4 T central memory and DN T cells. CONCLUSION: Our longitudinal profiling provides single-cell resolution of the shifts in immune cell dynamics following B cell depletion.