scRNA-seq reveals transcriptional dynamics of Encephalitozoon intestinalis parasites in human macrophages. scRNA-seq reveals transcriptional dynamics of Encephalitozoon intestinalis parasites in human macrophages

Microsporidia are single-celled intracellular parasites that cause opportunistic diseases in humans. Encephalitozoon intestinalis is a prevalent human-infecting species that invades the small intestine. Dissemination to other organ systems is also observed, and is potentially facilitated by macrophages. The macrophage response to infection and the developmental trajectory of the parasite are not well studied. Here we use single cell RNA sequencing to investigate transcriptional changes in both the host and parasite during infection. While a small population of infected macrophages mount a response, most remain transcriptionally unchanged, suggesting that the majority of parasites may avoid host detection. The parasite transcriptome reveals large transcriptional changes throughout the life cycle, providing a blueprint for parasite development. The stealthy microsporidian lifestyle likely allows these parasites to harness macrophages for replication and dissemination. Together, our data provide insights into the host response in primary human macrophages and the E. intestinalis developmental program. Overall design: Monocyte derived macrophages were isolated from four healthy human donors. The macrophages were infected with the human infecting species of microsporidia, Encephalitozoon intestinalis, over 3 hour post infection to 72 hours post infection and anaylzed using scRNAsequencing.

微孢子虫（Microsporidia）是一类单细胞胞内寄生虫，可引发人类机会性感染疾病。肠脑炎微孢子虫（Encephalitozoon intestinalis）是一种常见的人类感染性病原，主要侵袭小肠；该病原体还可播散至其他器官系统，其播散过程或由巨噬细胞介导促进。目前针对感染状态下巨噬细胞的宿主应答反应，以及该寄生虫的发育轨迹，相关研究尚不完善。本研究采用单细胞RNA测序（single cell RNA sequencing）技术，探究感染过程中宿主与寄生虫双方的转录组变化。研究发现，仅少量受感染的巨噬细胞会启动免疫应答，绝大多数受感染巨噬细胞的转录水平并未发生显著改变，这提示大部分寄生虫或可逃脱宿主的免疫识别。寄生虫的转录组分析显示，其整个生命周期中存在广泛的转录组变化，为寄生虫的发育进程提供了分子蓝图。这种隐秘的微孢子虫生存策略，或使其能够利用巨噬细胞完成自身的复制与播散。综上，本研究数据为原代人源巨噬细胞中的宿主应答反应，以及肠脑炎微孢子虫的发育程序提供了全新的认知。整体实验设计：从4名健康人类供者体内分离得到单核细胞源性巨噬细胞（monocyte derived macrophages）；将上述巨噬细胞使用肠脑炎微孢子虫进行感染，于感染后3小时至72小时期间取样，并通过scRNAsequencing完成分析。