Single cell approach to study host/enteric virus interaction in human mini-gut organoids

使用永生化的肠道上皮细胞系表征宿主/肠道病原体的相互作用并不能反映病原体和细胞内在免疫系统在人类肠道中所面临的复杂环境。事实上，肠道的特点是在隐窝/绒毛轴上存在多个特定的细胞谱系，这些细胞必须耐受共生菌群，但要为肠道病毒攻击做好准备。在这项建议中，我们将利用单细胞转录分析和可视化的活的迷你肠道器官在肠道病毒感染期间的免疫反应。我们将在肠上皮组织的背景下描述肠上皮细胞的固有免疫反应。这将使我们能够在单细胞水平上描述自然存在于人类肠道中的每一种单个细胞类型产生的抗病毒先天免疫反应，并表征感染和免疫反应如何在隐窝/绒毛轴组织的肠道上皮内在空间和时间内传播。在这个项目完成时，我们将开发一种生理培养系统，使我们能够解决病原体/上皮细胞之间的复杂相互作用。这将为我们研究宿主/病原体相互作用和肠道疾病提供前所未有的视角。

Characterization of host/enteric pathogens interactions using immortalized intestinal epithelial cell lines do not reflect the complex environment that both the pathogens and the cellular intrinsic immune system face in the human gut. Indeed, the intestinal tract is characterized by the presence of multiple specific cell lineages arranged within a crypt/villi axis, which must tolerate the commensal flora but be primed for enteric virus attacks. In this proposal, we will exploit both single cell transcriptomic analyses and visualization of immune response in live mini-gut organoids during enteric virus infection. We will characterize the intrinsic innate immune response of intestinal epithelial cells in the context of the intestinal epithelium organization. This will allow us to describe, at the single cell level, the antiviral innate immune response generated by each individual cell type naturally present in the human gut and to characterize how both infection and immune response spread in space and time within the crypt/villi axis organized gut epithelium. At the completion of this project we will have developed a physiological culture system allowing us to address the complex interplay between pathogen/epithelial cells. This will offer us unprecedented perspectives to study host/pathogen interactions and intestinal disease.