3D Ultrastructural segmentation of human microvasculature reveals new insights in pericyte-endothelial cell interactions

Introduction Capillary structure remains incompletely characterized at the nanoscale level. Advances in 3D electron microscopy datasets provide new opportunities to systematically examine microvascular architecture and cellular interactions. Methods We performed 3D image segmentation of human cerebral cortex microvasculature using the publicly available H01 Release dataset. This initial analysis focused on descriptive and quantitative characterization of the basement membrane, peg-and-socket cell interactions, and other subcellular features. Results We identified several novel structural features. In addition to known bidirectional peg-and-socket connections between pericytes (PCs) and endothelial cells (ECs), we observed similar structures between neighboring ECs and at interfaces where ECs form junctions with themselves. PC pegs showed an unexpected preference for proximity to EC nuclei and were enriched at PC edges. The PC endoplasmic reticulum (ER) frequently contacted the plasma membrane on the lumen-facing surface, particularly at sites corresponding to sockets of EC pegs. We also identified electron-lucent pockets (ELPs) at interfaces between ECs and PCs, as well as within the basement membrane. Discussion These findings expand current understanding of capillary ultrastructure by revealing previously unrecognized interactions between vascular cells and novel subcellular features. The observed structural features may have functional implications for signaling, stability, and vascular mechanics, warranting further investigation.