Genome-wide consensus transcriptional signatures identify synaptic pruning linking Alzheimer’s disease and epilepsy

Alzheimer’s disease (AD) and epilepsy (EP) share a complex bidirectional relationship, yet the molecular mechanisms underlying their comorbidity remain insufficiently explored. To identify potential consensus transcriptional programs across animal models and human patients with AD and EP, we conducted comprehensive genome-wide transcriptomic analyses of multiple datasets. Our investigation included mouse models of temporal lobe epilepsy (pilocarpine- and kainic acid-induced; n = 280), mouse models of AD (7 transgenic models expressing human tau or amyloid pathology; n = 257), and performed cross-species validation in human cohorts (EP: n = 176; AD: n = 253). Our unsupervised gene co-expression analysis revealed a highly conserved immune-related module across all models and patient cohorts. The hub consensus signatures of this module were centered around a microglial synaptic pruning pathway involvingTYROBP,TREM2, andC1Qcomplement components. Gene regulatory network analysis identifiedTYROBPas the key upstream hub signature. These hub consensus signatures showed consistent upregulation in both human AD and EP cohorts, preserved their regulatory relationship across species, and demonstrated strong diagnostic value. Computational modeling further demonstrated asymmetric sensitivity of synaptic pruning on neural network dynamics, with inhibitory synapse loss exerting disproportionately larger effects on excitation/inhibition (E/I) balance shifting it toward hyperexcitability and increasing neural network synchrony. Our findings indicated microglial complement-mediated synaptic pruning as a conserved central pathway linking neurodegeneration to epileptogenesis and suggested that targeting this pathway may offer therapeutic benefits for AD and EP comorbidity.