Structural Change of ApoE-Lipid Nanoparticles Alters Receptor-Mediated Endocytosis and Induces Endosomal Disruption

Apolipoprotein E (ApoE) is a key regulator of lipid metabolism that binds to lipid nanoparticle (LNP) surfaces to mediate cellular interactions. However, the ApoE-LNP behavior is highly dependent on the LNP composition, and the underlying mechanisms remain unclear. Here, we show that subtle alterations in LNP surface lipids profoundly reshape the ApoE-LNP structure and intracellular trafficking. Using cryogenic electron microscopy and live-cell imaging, we demonstrate that replacing 10 mol % 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) with a porphyrin-lipid conjugate induces highly faceted, irregular LNP membrane morphologies upon ApoE binding. These structural transitions alter receptor-mediated uptake, enhance endosomal disruption, promote cytosolic siRNA release, and ultimately trigger cell apoptosis. Through fluorescence lifetime imaging, we also demonstrate that ApoE promotes LNP intracellular disassembly. Overall, our findings identify lipid-driven structural remodeling of ApoE-LNPs as a critical determinant of their intracellular fate, offering mechanistic insights for the rational design of LNPs and new perspectives on ApoE's role in disease pathogenesis.