Network Preservation Analysis Reveals Dysregulated Synaptic Modules and Regulatory Hubs Shared Between Alzheimer’s Disease and Temporal Lobe Epilepsy

Background: There is increased prevalence of epilepsy in patients with Alzheimer’s disease (AD). Although shared pathological and clinical features have been identified, the underlying pathophysiology and cause-effect relationships are poorly understood. We aimed to identify commonly dysregulated groups of genes between these two disorders. Methods: Using publicly available transcriptomic data from hippocampal tissue of patients with temporal lobe epilepsy (TLE), late onset AD and non-AD controls, we constructed gene coexpression networks representing all three states. We then employed network preservation statistics to compare the density and connectivity-based preservation of functional gene modules between TLE, AD and controls and used the difference in significance scores as a surrogate quantifier of module preservation. Results: The majority (>90%) of functional gene modules were highly preserved between all coexpression networks, however several modules identified in the TLE network showed various degrees of preservation in the AD network compared to that of control. Of note, two synaptic signalling-associated modules and two metabolic modules showed substantial gain of preservation, while myelination and immune system-associated modules showed significant loss of preservation. The genes SCN3B and EPHA4 were identified as central regulatory hubs of the highly preserved synaptic signalling-associated module. GABRB3 and SCN2A were identified as central regulatory hubs of a smaller neurogenesis-associated module, which was enriched for multiple epileptic activity and seizure-related human phenotype ontologies. Conclusion: We conclude that these hubs and their downstream signalling pathways are common modulators of synaptic activity in the setting of AD and TLE, and may play a critical role in epileptogenesis in AD.