Mapping H3K27ac in in vitro differentiated resident memory CD8+ T cells. Mapping H3K27ac in in vitro differentiated resident memory CD8+ T cells

The networks of transcription factors (TFs) that control multipotency versus effector programs in intestinal resident memory T (TRM) cells are poorly understood. Mice with post-activation, conditional deletion of the TF Bcl11b in CD8+ T cells, infected with a food-born pathogen, had increased numbers of intestinal TRM cells, and their precursors and decreased splenic effector cells and circulating memory cells and precursors. Loss of circulating memory cells was in part due to increased intestinal homing of Bcl11b-/- circulating precursors with no major alterations in their programs. Bcl11b-/- memory CD8+ T cells had an impaired recall response despite their accumulation in the gut. Intestinal Bcl11b-/- TRM cells and their precursors manifested major alterations in the residency program, with diminished expression of multipotency program genes and upregulation of the effector program genes. Integration of transcriptomics with chromatin accessibility, activating histone marks and Bcl11b genome binding showed a link between the reduction in the multipotent program genes with regions of decreased chromatin accessibility and activating histone marks in Bcl11b-/- cells. In contrast, the effector program genes displayed increased activating epigenetic status. We propose that Bcl11b regulates tissue resident TRM program genes and is positioned upstream of Tcf1 and Blimp1 in regulation of multipotency versus effector TRM program, respectively. Rescuing experiments normalized the increased numbers of intestinal Bcl11b-/- TRM cells. Thus, Bcl11b is a frontrunner in the memory tissue residency program and acts early in lineage decision, promoting TRM cell multipotency and restricting effector function. Overall design: Examination of H3K27ac deposition in wild type and Bcl11b-deficient CD8+ Trm-like cells

目前对于调控肠道驻留记忆T（intestinal resident memory T, TRM）细胞多能性与效应性功能程序的转录因子（transcription factors, TFs）网络仍知之甚少。在食源性病原体感染的小鼠模型中，对CD8+ T细胞内的转录因子Bcl11b进行激活后条件性敲除，可导致肠道TRM细胞及其前体细胞数量增加，同时脾脏效应细胞、循环记忆细胞及其前体细胞的数量减少。循环记忆细胞的丢失部分源于Bcl11b敲除（Bcl11b-/-）的循环前体细胞向肠道的归巢增强，而其细胞程序未发生显著改变。尽管Bcl11b-/-记忆性CD8+ T细胞在肠道中大量蓄积，但其回忆应答（recall response）功能受损。肠道内的Bcl11b-/- TRM细胞及其前体细胞在驻留程序上出现显著改变：多能性程序相关基因的表达水平降低，而效应性功能程序相关基因的表达则出现上调。通过整合转录组学、染色质开放性、组蛋白激活修饰标记以及Bcl11b全基因组结合数据的分析发现，在Bcl11b-/-细胞中，多能性程序基因的表达下调与染色质开放性降低以及组蛋白激活修饰标记减少的区域存在关联。与之相反，效应性功能程序相关基因则呈现出更高的激活型表观遗传状态。我们提出，Bcl11b可调控组织驻留TRM细胞的程序基因，并分别位于调控多能性与效应性功能TRM程序的Tcf1与Blimp1的上游。挽救实验可使肠道内Bcl11b-/- TRM细胞数量异常升高的表型恢复正常。综上，Bcl11b在记忆性组织驻留程序中发挥核心调控作用，并在细胞谱系决策早期即参与调控：一方面促进TRM细胞的多能性，另一方面则抑制其效应性功能。实验整体设计：检测野生型与Bcl11b缺陷型CD8+ TRM样细胞中的H3K27ac沉积情况。