Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer's disease

The blood-brain barrier (BBB) is primarily manifested by a variety of physiological properties of brain endothelial cells (ECs), but the molecular foundation for these properties remains incompletely clear. Here, we generate a comprehensive molecular atlas of adult brain ECs using acutely purified mouse ECs and integrated multi-omics. Using RNA-seq and proteomics, we identify the transcripts and proteins selectively enriched in brain ECs and demonstrate that they are partially correlated. Using single-cell RNA-seq, we dissect the molecular basis of functional heterogeneity of brain ECs. Using integrative epigenomics and transcriptomics, we determine that TCF/LEF, SOX, and ETS families are top-ranked transcription factors regulating the BBB. We then validate the identified brain EC-enriched proteins and transcription factors in normal mouse and human brain tissue, and assess their expression changes in mice with Alzheimer's disease. Overall, we present a valuable resource with broad implications for the BBB regulation and treatment of neurological disorders. Bulk-RNA-seq and ATAC-seq were performed on mouse brain, lung and liver endothelial cells. Single-cell RNA-seq was performed on adult mouse brain endothelial cells.血脑屏障（blood-brain barrier, BBB）主要由脑内皮细胞（brain endothelial cells, ECs）的多种生理特性所体现，但这些特性的分子基础尚未完全阐明。本研究利用急性纯化的小鼠脑内皮细胞结合整合多组学技术，构建了成年脑内皮细胞的完整分子图谱。通过RNA测序（RNA-seq）与蛋白质组学，我们鉴定出脑内皮细胞中选择性富集的转录本与蛋白质，并证实二者存在部分相关性。借助单细胞RNA测序（single-cell RNA-seq），我们解析了脑内皮细胞功能异质性的分子基础。通过整合表观基因组学与转录组学，我们确定TCF/LEF、SOX及ETS家族是调控血脑屏障的顶级转录因子。随后，我们在正常小鼠及人脑组织中验证了所鉴定的脑内皮细胞富集蛋白质与转录因子，并评估了阿尔茨海默病（Alzheimer's disease）模型小鼠体内这些分子的表达变化。总体而言，本研究提供了一项具有重要价值的研究资源，对血脑屏障调控及神经系统疾病的治疗具有广泛的应用前景。本研究对小鼠脑、肺及肝脏内皮细胞开展了批量RNA测序（bulk-RNA-seq）与转座酶可及性染色质测序（ATAC-seq），并对成年小鼠脑内皮细胞进行了单细胞RNA测序。