The interaction of UBR4, LRP1, and OPHN1 in refractory epilepsy: Drosophila model to investigate the oligogenic effect on epilepsy

Abstract

Refractory epilepsy is an intractable neurological disorder that can be associated with oligogenic/polygenic etiologies. Through trio-based whole-exome sequencing analysis, we identified a clinical case of refractory epilepsy with three candidate gene variants: UBR4, LRP1, and OPHN1. Utilizing the Gal4-UAS system and double-balancer tool, we generated single, double, and triple knockdown Drosophila models to investigate the interactions of the three candidate genes. Seizure behavioral experiments combined with logistic regression analysis revealed the individual epileptogenicity and significant synergistic epileptogenic effects of the three mutations. By constructing a SHAP-XGBoost machine learning model integrating seizure behavior data with knockdown efficiency metrics, we discovered that LRP1 mutation served as the primary effector in the oligogenic system. Based on transcriptome analysis, main related processes of oxidative stress and metabolic imbalance together with expressional dysregulation separately of 48, 52, and 43 epilepsy-associated genes were discovered to confirm the epileptogenicity of OPHN1 knockdown, UBR4-LRP1 knockdown, and UBR4-LRP1-OPHN1 knockdown. Up-regulation of COX7AL and ND-B8 enriched in metabolic pathways and down-regulation of Diedel enriched in extracellular space component were indicated to be responsible for the significant epileptogenicity of the oligogenic knockdown. For this clinical instance, epileptic pharmacoresistance was considered to be triggered by a combination of KIF gene family, SLC gene family, and ASIC gene family. This study established a novel framework to clarify the multiple genetic structure of epileptogenicity in refractory epilepsy with oligogenic background, which could be critical to translational medicine and precision therapy development.