Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [ATAC-Seq 2]

As “effector” cells, B lymphocytes make antibodies. They also regulate immune functions through ligand-receptor interactions. The limited understanding of regulatory roles of B cells prompted us to develop a workflow that profiles B cell ligand and receptor expression, maps in silico interactions involving ligands with high “specificity scores”, validates the function of top ligand-receptor interactions, and unveils transcription regulation of specific ligands. Using this unbiased approach, here we report the regulatory functions of a new subset of murine B cells that express BATF3 as a hallmark transcription factor. BATF3+ B cells, as generated upon B cell activation by innate TLR and adaptive CD40 and IL-21 receptor signals, lose their effector cell function (making class-switched antibodies) while expressing new ligands, most notably cytokine IL-27 and chemokine CXCL10. As elicited by viral infection and immunization, IL-27+CXCL10+ B cells target effector B cells through the IL-27 receptor and, together with IFNg, optimize the antibody response and anti-viral immunity. Also appearing in tumors and retained there through the autocrine CXCL10-CXCR3 interaction, they enhance B cell expression of immune checkpoint PD-L1 and suppress anti-tumor immunity. Thus, we have identified new regulatory B cells and provided a paradigmatic framework to investigate immune cell communications. Overall design: B cells from Batf3 wildtype and knockout mice were stimulated with either LPS or LPS plus anti-CD40 and IL-21 (LA21). Regions of open chromatin was accessed and compared between conditions using ATAC-seq.

作为效应细胞（effector），B淋巴细胞可合成抗体，同时通过配体-受体相互作用调控免疫功能。鉴于当前对B细胞调控功能的认知仍存在局限，我们开发了一套标准化分析流程，可实现B细胞配体与受体表达谱分析、对携带高"特异性评分（specificity score）"的配体所参与的虚拟（in silico）相互作用进行预测映射、验证核心配体-受体相互作用的功能，并揭示特定配体的转录调控机制。借助这一无偏分析策略，我们在此报道了一类以BATF3作为标志性转录因子的新型小鼠B细胞亚群的调控功能。BATF3阳性（BATF3+）B细胞可在先天Toll样受体（TLR）信号、适应性CD40与IL-21受体信号激活B细胞后诱导产生，这类细胞会丧失效应细胞功能（不再产生类别转换抗体），同时表达新型配体，其中尤以细胞因子IL-27和趋化因子CXCL10为代表。在病毒感染与免疫接种过程中诱导产生的IL-27阳性、CXCL10阳性（IL-27+CXCL10+）B细胞可通过IL-27受体靶向效应B细胞，并与干扰素γ（IFNγ）协同优化抗体应答与抗病毒免疫。该细胞亚群同样可在肿瘤微环境中出现，并通过自分泌CXCL10-CXCR3相互作用驻留于肿瘤内，可上调B细胞的免疫检查点程序性死亡配体1（PD-L1）表达，并抑制抗肿瘤免疫。综上，我们鉴定出一类新型调控性B细胞，并为研究免疫细胞间的通讯网络提供了范式化研究框架。实验整体设计：分别使用脂多糖（LPS）或脂多糖联合抗CD40与IL-21（LA21）刺激来自Batf3野生型与敲除型小鼠的B细胞；通过转座酶可及性测序（ATAC-seq，Assay for Transposase-Accessible Chromatin using sequencing）对不同处理组的开放染色质区域进行检测并开展比较分析。