Loss of Elp3 impairs the immune response to helminths by blocking intestinal tuft cell differentiation. Loss of Elp3 impairs the immune response to helminths by blocking intestinal tuft cell differentiation

Intestinal tuft cells are critical in anti-helminth immunity by producing IL-25, which triggers IL-13 secretion by activated group 2 innate lymphoid cells (ILC2s) in order to ultimately expand both goblet and tuft cells. Translational reprogramming is involved in intestinal tuft cell differentiation but the role of tRNA modifications in this process is unknown. We show here that epithelial Elp3, a tRNA-modifying enzyme, promotes tuft cell differentiation and is consequently critical for IL-25 production, ILC2 activation, goblet cell expansion and control of N. brasiliensis infection in mice. Elp3 is essential for the IL-13-dependent induction of some glycolytic enzymes such as Hexokinase 1 and Aldolase A and consequently links specific metabolic pathways to tuft cell differentiation. Importantly, loss of epithelial Elp3 in the intestine blocks the translation of Nprl2, a mTORC1 inhibitor, which consequently enhances mTORC1 activation and stabilizes Atf4 in both transit amplifying and progenitor cells. Likewise, Atf4 overexpression in mouse intestinal epithelium blocks tuft cell differentiation and impairs the control of intestinal helminth infection. Collectively, our data define Atf4 as a negative regulator of tuft cell differentiation and provide insights into mechanisms through which some tRNA modifications promote a type 2 immune response to parasites in the intestine. Overall design: To investigate the role of the tRNA-modifying enzyme Elp3 in tuft cell differentiation, we performed a Single Cell RNA-sequencing on intestinal epithelial cells from Elp3WT vs Elp3ΔIEC mice. Mice were treated overnight with rIL-13 in order to induce tuft cell differentiation.

肠道簇状细胞（intestinal tuft cells）通过分泌IL-25在抗蠕虫免疫中发挥关键作用：IL-25可激活2型先天淋巴样细胞（group 2 innate lymphoid cells, ILC2s），促使其分泌IL-13，最终促进杯状细胞与簇状细胞的增殖与扩增。翻译重编程参与肠道簇状细胞的分化过程，但tRNA（transfer RNA）修饰在该过程中的具体作用尚未明确。本研究证实，上皮来源的Elp3作为一种tRNA修饰酶，可促进簇状细胞分化，进而对IL-25分泌、ILC2激活、杯状细胞扩增以及小鼠感染巴西日圆线虫（Nippostrongylus brasiliensis, N. brasiliensis）后的感染控制至关重要。Elp3对于IL-13依赖的部分糖酵解酶（如己糖激酶1（Hexokinase 1）、醛缩酶A（Aldolase A））的诱导表达不可或缺，从而将特定代谢通路与簇状细胞分化建立功能关联。值得注意的是，肠道上皮细胞中Elp3的缺失会阻断mTORC1抑制剂Nprl2的翻译过程，进而增强哺乳动物雷帕霉素靶蛋白复合物1（mammalian target of rapamycin complex 1, mTORC1）的激活，并在短暂扩增细胞（transit amplifying cells）与祖细胞中稳定激活转录因子4（Activating Transcription Factor 4, Atf4）的表达。同样地，在小鼠肠道上皮细胞中过表达Atf4会阻断簇状细胞分化，并削弱机体对肠道蠕虫感染的免疫控制能力。综上，本研究数据确定Atf4为簇状细胞分化的负调控因子，并揭示了部分tRNA修饰促进肠道寄生虫2型免疫应答的潜在机制。实验设计：为探究tRNA修饰酶Elp3在簇状细胞分化中的作用，我们对Elp3野生型（Elp3WT）与Elp3肠道上皮特异性敲除（Elp3ΔIEC）小鼠的肠道上皮细胞开展了单细胞RNA测序（Single Cell RNA-sequencing）。所有小鼠均经重组IL-13（recombinant IL-13, rIL-13）过夜处理，以诱导簇状细胞分化。