Structural and Synaptic Dysregulation Drives Network Vulnerability in APOE4 Human Neuronal Networks

Synaptic failure and associated neuronal network dysfunction are key pathological processes involved in the early stages of Alzheimer’s disease (AD). A better understanding of the specific synaptic pathways and network topologies that drive disease vulnerability is therefore essential for the development of a targeted therapeutic intervention. In the present study, we aimed to determine how defined synaptic pathways and connectivity patterns shape the emergence and progression of the structural and functional network dynamics of human neuronal networks with inherent vulnerability to AD. We performed longitudinal microelectrode array recordings, assessed excitatory and inhibitory activity, quantified neurite growth, and performed proteomic analyses of synaptosomes from human induced pluripotent stem cell-derived neuronal networks carrying homozygous apolipoprotein E epsilon 4 (APOE4), the strongest genetic risk factor for developing late-onset AD. This integrated approach enabled multiscale characterization of synaptic alterations, structural maturation, and functional network dynamics associated with AD vulnerability. Compared to isogenic homozygous APOE3 networks, we found that APOE4 drives a distinct topological regime, characterized by high assortativity combined with low transitivity, which reflects a compensatory organization with reduced redundancy and flexibility, consistent with an intrinsically fragile network structure. APOE4 networks exhibited reduced firing rates, dynamic excitatory and inhibitory imbalance, impaired synchronization, absence of network bursting, and reduced global routing efficiency. Despite retaining small-world properties indicative of baseline information processing capacity, the topological and functional profile of APOE4 networks suggests a reliance on compensatory mechanisms associated with elevated metabolic cost and increased susceptibility to pathological spread. Structurally, APOE4 networks displayed reduced dendritic length, branching, and total dendrite area, accompanied by dysregulation of synaptic organization and signaling, ion dynamics, and intracellular signaling pathways. Together, these findings establish that APOE4 drives a multiscale reorganization of neuronal networks that not only mirrors synaptic alterations identified in patients, but also contextualizes these changes within network-level dynamics, advancing a more comprehensive understanding of early AD pathology.