Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (Single-cell RNA-Seq Batch_2)

We have developed a novel in vitro protocol for the derivation of bona fide Pharyngeal Endoderm (PE) cells from hESCs. We demonstrated that our PE cells robustly express Pharyngeal Endoderm markers, they are transcriptionally similar to PE cells isolated from in vivo mouse development and represent a transcriptionally homogeneous population. Importantly, we elucidated the contribution of Retinoic Acid in promoting a transcriptional and epigenetic rewiring of PE cells. In addition, we defined the epigenetic landscape of PE cells by combining ATAC-Seq and ChIP-Seq of histone marks. We performed a scRNA-Seq analysis of Definitive Endoderm (Day 2), Anterior Foregut Endoderm (Day 3 and Day 5) and Pharyngeal Endoderm (Day 5 + RA) cells.

本研究建立了一套全新的体外实验方案，可从人类胚胎干细胞（human embryonic stem cells, hESCs）中诱导得到纯正的咽内胚层（Pharyngeal Endoderm, PE）细胞。研究证实，该方法获得的PE细胞可稳定表达咽内胚层标志物，其转录组特征与体内分离的小鼠咽内胚层细胞高度相似，且属于转录均一的细胞群体。尤为重要的是，本研究阐明了视黄酸（Retinoic Acid, RA）在促进PE细胞转录组与表观基因组重编程中的调控作用。此外，本研究通过结合组蛋白修饰的转座酶可及性测序（ATAC-Seq）与染色质免疫共沉淀测序（ChIP-Seq），明确了PE细胞的表观遗传图谱。本研究还对定型内胚层（第2天）、前肠前端内胚层（第3天、第5天）以及咽内胚层（第5天 + 视黄酸处理）细胞开展了单细胞RNA测序（scRNA-Seq）分析。