Single-Cell RNA Sequencing Reveals Disease Stage-Dependent Transcriptomic Profiles of Regulatory B Cells in Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune disease associated with abnormal activation of immune cells. Regulatory B (Breg) cells are a B cell subset that negatively regulate immune responses via secretion of immunoregulatory cytokines interleukin (IL)-10, IL-35, and transforming growth factor (TGF)-β. We had previously shown that in lupus-prone MRL/lpr mice, pre-disease Breg cells were more potent in suppressing autoimmunity than active-disease Breg cells. In this study, using single-cell RNA (scRNA) sequencing, we profiled ~10,000 Breg cells from female MRL/lpr mice at the pre-disease (6–8 weeks of age) vs. active-disease (10–12 weeks of age) stages. Based on known markers of Breg subsets, scRNA analysis identified respective clusters as transtional-2 marginal zone precursor B cells (T2-MZP), marginal zone B cells (MZB), transitional 1 B cells (T1), germinal center B cells (GC), and B1 B cells. Our data showed that the pre-disease Breg cells were predominantly T2-MZP and MZB cells. Follicular B cells outside the marginal zone, on the other hand, are significantly increased in the active-disease stage. Two long noncoding RNAs (lncRNAs), Malat1 and Xist, were significantly increased in active-disease Breg cells, where the expression of Lglas3, Slpi, and Spp1 was also increased. Notably, active-disease Breg cells exhibited an exhausted phenotype with increased expression of T-bet (Tbx21). Collectively, our findings suggest that the SLE disease stage-dependent functions of Breg cells are regulated at the transcriptional level. In future experiments, we will determine whether the immunosuppressive functions of active-disease Breg cells can be restored by knocking down the differentially overexpressed genes.