Specific traits of the B cell response to self-antigens revealed by single cell transcriptomics

In an autoimmune environment, B cells spontaneously participate and are selected in germinal centers (GC). In previous work, we investigated epitope spreading in a mixed bone marrow chimera model that combines B cells from lupus-like mice with those from wild type (WT) B6 mice (Degn et al Cell 2017). In the current study, we identify novel biomarkers of autoimmune B cells at the population and single cell level. Cohorts of autoimmune and WT immunized chimeric mice were prepared. To track WT-derived B cells, we used the tamoxifen inducible AID-CreERT2-EYFP mice. WT chimeras were immunized and boosted. Splenic B cells were sorted based EYFP+ signal and processed for droplet-based gene expression and BCR repertoire single cell RNAseq. To detect specific traits of autoreactive B cells relative to immunized, unsupervised cluster analysis, differential gene expression and pseudotime analysis were used. Results show higher antibody repertoire diversity in the autoimmune relative to immune B cells, but striking similarity for transcriptomic usage. However, distinct gene expression was identified for the autoreactive B cells such as CXCL10 usage by GC B cells and SLPI expression by autoreactive plasma cells. Importantly, we were able to identify DN2- and DN4-like memory B cells in both conditions. DN2 cells, presumed to derive directly from naïve B cells, have been recently pointed as a source of pathogenic extrafollicular antibody secreting cells in humans. Overall, results reveal the variety of characteristics that B cells, in their many states, adopt in the response to self and should open the way to new approaches to control their pathogenicity in autoimmune disease.