Gene expression profile of murine thymic B cells in the presence or absence of CD40 signaling

The thymus contains some B cells that are located at the corticomedullary junction. We found that these thymic B cells express and present the water channel protein AQP4 and are necessary and sufficient to mediate the negative selection of AQP4-reactive thymocytes. In order to express and present AQP4, thymic B cells need to be licensed through a CD40 signal. Here, we tested the significance of CD40 signaling in thymic B cells for the expression and presentation of distinct autoantigens (besides AQP4) to orchestrate thymocyte selection for these autoantigens. 2000 B cells per sample were sorted from the thymus of naive, untreated wild type (WT, C57BL/6, Charles River) or CD40KO (JAX strain 002927) mice aged 6-8 weeks (5 mice per genotype) and then subjected to bulk RNAseq. After the initial run, the same libraries were sequenced again to increase overall sequencing depth.胸腺中存在一类定位于皮髓质交界处（corticomedullary junction）的B细胞。本研究发现，此类胸腺B细胞可表达并呈递水通道蛋白AQP4（Aquaporin 4），且是介导AQP4反应性胸腺细胞阴性选择的必要且充分条件。若要实现AQP4的表达与呈递，胸腺B细胞需要通过CD40信号获得活化许可。为探究胸腺B细胞的CD40信号通路在表达及呈递除AQP4外的其他自身抗原、进而协调针对这些自身抗原的胸腺细胞选择过程中的意义，我们从6~8周龄的未致敏、未经处理的野生型（WT, C57BL/6, Charles River）或CD40基因敲除小鼠（CD40KO，JAX品系002927）的胸腺中分选每份样本所需的2000个B细胞（每个基因型使用5只小鼠），随后对样本进行批量RNA测序（bulk RNAseq）。首轮测序完成后，我们对同一文库再次进行测序以提升整体测序深度。