A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture

Vascular endothelial cells (ECs) derived from the central nervous system (CNS) variably lose their unique barrier properties during in vitro culture, hindering the development of robust assays for BBB function, including drug permeability and extrusion assays. In previous work (Sabbagh et al., 2018) we characterized transcriptional and accessible chromatin landscapes of acutely isolated CNS ECs. In this report, we compare transcriptional and accessible chromatin landscapes of acutely isolated CNS ECs versus CNS ECs in short-term in vitro culture. We observe that standard culture conditions are associated with a rapid and selective loss of BBB transcripts and chromatin features, as well as a greatly reduced level of beta-catenin signaling. Interestingly, forced expression of a stabilized derivative of beta-catenin, which in vivo leads to a partial conversion of non-BBB CNS ECs to a BBB-like state, has little or no effect on gene expression or chromatin accessibility in vitro. RNA-seq and ATAC-seq of primary brain EC culture血管内皮细胞（vascular endothelial cells, ECs）源自中枢神经系统（central nervous system, CNS），在体外培养过程中会不同程度地丧失其独特的屏障特性，这阻碍了血脑屏障（blood-brain barrier, BBB）功能稳健检测方法的开发，包括药物通透性及外排检测实验。既往研究（Sabbagh等，2018年）中，我们已对急性分离的中枢神经系统血管内皮细胞的转录组与染色质开放景观进行了表征。本研究中，我们对比了急性分离的中枢神经系统血管内皮细胞与短期体外培养的中枢神经系统血管内皮细胞的转录组及染色质开放景观。我们发现，标准培养条件会导致血脑屏障相关转录本与染色质特征快速且选择性地丧失，同时伴随β-连环蛋白（beta-catenin）信号通路活性显著下调。有趣的是，尽管在体内环境中，β-连环蛋白的稳定型突变体的强制表达可将非血脑屏障型中枢神经系统血管内皮细胞部分转化为类血脑屏障表型，但在体外培养体系中，其对基因表达或染色质开放度几乎无影响。本数据集包含原代脑源性血管内皮细胞培养的RNA测序（RNA-seq）与转座酶可及性测序（ATAC-seq）相关数据