Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [DNase-seq]. Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [DNase-seq]

Lymphoid tissue inducer (LTi) cells, known to be critical for the generation of secondary lymphoid tissues, are the founding member of innate lymphoid cells (ILCs). However, how the development and functions of this ILC subset are regulated is far from clear. In this study, we discovered a striking role of the transcription factor TCF-1 in the development of Peyer’s patches (PPs) but not lymph nodes (LNs). Despite TCF-1 is critical for ILC development at multiple stages, we found normal development of LTi cells in TCF-1-deficient mice indicating that dysfunction of these LTi cells led to the deficiency in Peyer’s patches formation. Through bulk and single cell RNA-Seq, we found differential gene expression patterns between LTi cells from the PPs, LNs and the small intestine laminal propria (siLP), and an important role of TCF-1 in regulating the expression of lymphotoxin (LT) specifically in PP LTi cells. Mechanistically, TCF-1 may regulate Lta indirectly through promoting the expression of GATA3, a critical transcription factor in regulating LTi functions. LTβR agonist injection during the embryonic stage partially rescued the formation of PPs in the TCF-1-deficient mice. Thus, a dose effect of LT expression in LTi cells regulated by TCF-1 contributes to a differential regulation of organogenesis of distinct secondary lymphoid structures. Overall design: Live Lin-CD127+ KLRG1-NK1.1-NKp46-CCR6+ lymphoid tissue inducer (LTi) cells from Peyer's patches of Tcf7+/+and Tcf7fl/flRorcCre mice were used for Dnase-Seq analysis.

淋巴组织诱导细胞（Lymphoid tissue inducer, LTi）是介导次级淋巴组织生成的关键细胞，同时也是先天淋巴细胞（innate lymphoid cells, ILCs）的创始成员。然而，这一ILC亚群的发育与功能调控机制仍有待深入阐明。本研究发现，转录因子TCF-1在派尔集合淋巴结（Peyer’s patches, PPs）的发育中发挥显著调控作用，但对淋巴结（lymph nodes, LNs）并无此类效应。尽管TCF-1在多个阶段对ILC的发育至关重要，我们却在TCF-1缺陷小鼠中观察到LTi细胞发育正常，这提示此类LTi细胞的功能异常是导致派尔集合淋巴结生成缺陷的核心原因。通过批量RNA测序（bulk RNA-Seq）与单细胞RNA测序（single cell RNA-Seq），我们发现源自派尔集合淋巴结、淋巴结及小肠固有层（small intestine laminal propria, siLP）的LTi细胞存在差异化基因表达谱，且TCF-1可特异性调控派尔集合淋巴结来源LTi细胞的淋巴毒素（lymphotoxin, LT）表达。从机制层面来看，TCF-1或可通过促进GATA3的表达间接调控Lta，而GATA3是调控LTi细胞功能的关键转录因子。胚胎时期注射淋巴毒素β受体（lymphotoxin β receptor, LTβR）激动剂可部分挽救TCF-1缺陷小鼠的派尔集合淋巴结生成缺陷。由此可见，TCF-1调控的LTi细胞中LT表达的剂量效应，是不同次级淋巴组织器官发生差异化调控的重要分子基础。整体实验设计：从Tcf7+/+及Tcf7fl/flRorcCre小鼠的派尔集合淋巴结中分离得到活的Lin-CD127+KLRG1-NK1.1-NKp46-CCR6+淋巴组织诱导细胞（LTi），并将其用于脱氧核糖核酸酶测序（DNase-Seq）分析。