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.