Network Topology reveals disrupted AMPA receptor stabilization leads to an impaired LTD in epileptic synapses

Cognitive comorbidities in epilepsy patients may be the result of synaptic alterations and impaired synaptic signalling. Electrophysiological evidence demonstrates that epileptic synapses undergo a GluN2B-dependent metaplastic shift, where a low-frequency stimulation protocol unexpectedly induced long-term potentiation (LTP) rather than long-term depression (LTD). However, the downstream postsynaptic structural cascade responsible for this functional impairment remains unresolved. To elucidate the molecular architecture driving this shift, this study employed an in silico protein-protein interaction network approach using Cystoscape. A baseline intersection network of LTD and epilepsy-associated genes were constructed, anchored with GRIN2B, and topologically ranked to identify hub proteins. This analysis identified a core module biased toward synaptic potentiation, dominated by the kinase CAMK2A, AMPA receptor subunits, and auxiliary Transmembrane AMPA Receptor Regulatory Proteins (TARPs) and CNIH2. These provided a structural basis for the prolonged receptor retention and delayed deactivation kinetics characteristic of epileptic synapses. Mapping the LTD-execution machinery against this interactome revealed that calcineurin was topologically segregated and lacks direct connectivity from the central AMPA receptor complex. Further studies would be required to test and confirm the involvement of these proteins. To experimentally validate these in silico findings, human transcriptomic data from cortical and hippocampal tissues of drug-resistant epilepsy patients was also analyzed which confirmed the significant upregulation of CNIH2 and CACNG2 in both tissue types. The cross-validation with patient transcriptomic data, demonstrated that the epileptic synapse undergoes a pathological shift. Hence, the upregulation of the auxiliary proteins functionally overpowers the established LTD machinery and prevents LTD consolidation.