Bcl6 is a subset defining transcription factor of Lymphoid Tissue inducer-like ILC3

Innate lymphoid cells (ILC) are tissue-resident effector cells with important roles in tissue homeostasis, protective immunity and inflammatory disease. Current nomenclature divides ILC into subsets based on the expression of master transcription factors and effector cytokine programs. In mucosal barrier tissues, group 3 ILC (ILC3) have been defined by the expression of the master transcription factor RORgt. However, ILC3 can be further subdivided into two major subsets – natural cytotoxicity receptor-expressing (NCR+) ILC3 and lymphoid tissue inducer (LTi)-like ILC3 which share type 3 effector modules but also exhibit significant ontological, transcriptional, phenotypic and functional heterogeneity. In particular, LTi-like ILC3 exhibit effector functions not typically associated with other RORgt-expressing lymphocytes, provoking the hypothesis that other master transcription factors may contribute to LTi-like ILC3 biology. Here we identify Bcl6 as an LTi-like ILC3 associated transcription factor in both mice and humans. Deletion of Bcl6 led to dysregulation of the LTi-like ILC3 transcriptional program and changes to subset-specific phenotypic markers and effector functions. Strikingly, loss of Bcl6 enhanced expression of the type 3 effector cytokines IL-17A and IL-17F in LTi-like ILC3, which was found to be in part dependent upon the commensal microbiota. Together these findings implicate Bcl6 as an ILC3 subset-defining transcription factor and part of a network that confers phenotype and function on LTi-like ILC3. Our study further provides a missing link to redefine analogous immune modules in innate and adaptive lymphocyte responses. Comparative gene expression analysis from RNA-seq data obtained from sorted LTi-like ILC3 and NCR+ ILC3 from the mLN and small intestine of Rorc-Cre Bcl6-fl/fl mice and Bcl6-fl/fl controls.

固有淋巴细胞（innate lymphoid cells, ILC）是定居于组织的效应细胞，在组织稳态、保护性免疫及炎症性疾病中发挥关键作用。当前的命名体系基于主转录因子（master transcription factors）的表达模式与效应细胞因子程序（effector cytokine programs），将ILC划分为不同功能亚群。在黏膜屏障组织（mucosal barrier tissues）中，第三组固有淋巴细胞（group 3 ILC, ILC3）的定义依据为其主转录因子RORγt（RORgt）的表达。然而，ILC3可进一步细分为两大核心亚群：表达自然细胞毒性受体（natural cytotoxicity receptor, NCR）的（NCR+）ILC3，以及淋巴组织诱导物（lymphoid tissue inducer, LTi）样ILC3；二者共享3型效应模块（type 3 effector modules），但同时存在显著的发育起源、转录、表型及功能异质性。尤为值得关注的是，LTi样ILC3所具备的效应功能通常与其他表达RORγt的淋巴细胞无关，这一现象催生了相关假说：其他主转录因子可能参与调控LTi样ILC3的生物学特性。本研究鉴定出B细胞淋巴瘤因子6（Bcl6）为小鼠与人类中均存在的、与LTi样ILC3相关的转录因子。敲除Bcl6会导致LTi样ILC3的转录程序失调，并改变亚群特异性的表型标志物与效应功能。令人意外的是，Bcl6的缺失会增强LTi样ILC3中3型效应细胞因子IL-17A与IL-17F的表达，且该效应在一定程度上依赖于共生菌群（commensal microbiota）。综上，本研究结果证实Bcl6是定义ILC3亚群的关键转录因子，亦是赋予LTi样ILC3表型与功能的调控网络的组成部分。本研究还为重新定义固有免疫与适应性淋巴细胞应答中的相似免疫模块提供了此前缺失的关键环节。本研究通过分选获取了Rorc-Cre介导的Bcl6条件性敲除（Bcl6-fl/fl）小鼠及Bcl6-fl/fl对照小鼠的肠系膜淋巴结（mesenteric lymph node, mLN）与小肠组织中的LTi样ILC3及NCR+ ILC3，对其RNA测序（RNA-seq）数据开展了比较基因表达分析。