The development of mouse trophoblast cells at the single cell level

The placenta is a poorly understood yet vital support organ. Transcriptome analysis at single cell resolution can help us understand cell compositions, developmental processes, and physiological functions. Both mice and humans have the hemochorial placenta. Profiling the single cell transcriptome of the mouse placenta is necessary for deepening our knowledge of mammalian placentation.We systematically profiled single cell transcriptomes of mouse placentae every day from E7.5 to E14.5. After stringent filtering, 15682 mouse trophoblast cells were subjected to following transcriptome analysis. We noted that trophoblast cells underwent 3 main differentiation stages: E7.5-E8.5, E9.5-E10.5, and E11.5-E14.5. With the help of advanced computational technologies from Velocyto, PAGA, monocle, and SCENIC, we have updated the recognitions of several developmental events. Firstly, P-TGCs are suggested to only derive from EPC like cells. Secondary, sinusoid trophoblast and spongiotrophoblast all derived from EPC cells, and their cell fates have been determined before the chorioallantoic fusion. Sinusoid trophoblast cells were not derived from chorion. Thirdly, SpA-TGCs were suggested to be differentiated from spongiotrophoblast cells via Gly-T cells. Furthermore, new transcription factors have been found to play roles during the differentiation of trophoblast cells. Lastly, the expression of Ifnlr1 in chorion branch cells gradually increased during placentation, which reconfirmed that mature placenta can defend the Zika virus (ZIKV) through IFN signaling. We clarified the developmental histories of mouse trophoblast cells at the branch level, especially the differentiation of sinusoid branch trophoblast cells. Meanwhile, we offered a convincing data resource for the study of mammalian placentation and etiology analysis of pregnancy-associated diseases. Single cell transcriptomes of mouse placentae that were collected at one-day intervals between E7.5 and E14.5 NOTE: The MPL39603-*.csv,MTR15682-*.csv, UMAP-MPL39603.csv, UMAP-MTR15682.csv, UMAP-MTR-E78-3529.csv files (included in the 10x_V*_processed_data.tar.gz) belong to the GSM4725071 - GSM4725071, and V3MPL30518-*.csv, V3MTR8067-*.csv files belong to the GSM6744596 - GSM6744600 samples.胎盘是一种尚未被充分阐释却至关重要的支持性器官。单细胞分辨率下的转录组分析，有助于解析其细胞组成、发育进程与生理功能。小鼠与人类均拥有血绒毛膜胎盘（hemochorial placenta）。对小鼠胎盘开展单细胞转录组谱型分析，是深化我们对哺乳动物胎盘发育认知的必要途径。 本研究系统采集了小鼠胚胎发育第7.5天（E7.5）至第14.5天（E14.5）每日的胎盘样本，完成单细胞转录组谱型分析。经严格质量过滤后，共保留15682个小鼠滋养层细胞用于后续转录组分析。研究发现，小鼠滋养层细胞主要经历三个分化阶段：E7.5-E8.5、E9.5-E10.5及E11.5-E14.5。 借助Velocyto、PAGA、Monocle及SCENIC等先进计算分析技术，本研究更新了对若干胎盘发育事件的认知：其一，P-TGCs仅由类EPC细胞分化而来；其二，窦状滋养层细胞与海绵滋养层细胞均源自EPC细胞，二者的细胞命运在绒毛膜尿囊融合前便已确定，且窦状滋养层细胞并非来源于绒毛膜组织；其三，SpA-TGCs经由Gly-T细胞由海绵滋养层细胞分化而来；此外，本研究还发现了若干在滋养层细胞分化过程中发挥调控作用的新型转录因子；最后，胎盘发育进程中，绒毛膜分支细胞内Ifnlr1的表达水平逐渐升高，这进一步证实成熟胎盘可通过干扰素（IFN）信号通路抵御寨卡病毒（ZIKV）。 本研究阐明了小鼠滋养层细胞在分支层面的发育轨迹，尤其是窦状分支滋养层细胞的分化过程。同时，本研究为哺乳动物胎盘发育研究以及妊娠相关疾病的病因学分析提供了可靠的数据资源。 本研究获取了E7.5至E14.5期间每日采集的小鼠胎盘单细胞转录组数据。 注：包含于10x_V*_processed_data.tar.gz压缩包内的MPL39603-*.csv、MTR15682-*.csv、UMAP-MPL39603.csv、UMAP-MTR15682.csv及UMAP-MTR-E78-3529.csv文件，对应GSM4725071样本；V3MPL30518-*.csv与V3MTR8067-*.csv文件则对应GSM6744596至GSM6744600样本。