Protective effect of CACNA1A deficiency in oligogenic refractory epilepsy with CACNA1A‐CELSR2 digenic mutations

Abstract Objective The vast majority of refractory epilepsy cases have a complex oligogenic/polygenic origin, which presents a challenge to precision medicine in individual patients. Nonetheless, the high workload and lack of effective guidelines have limited the number of in‐depth animal studies. Methods Whole‐exon sequencing identified a case with refractory epilepsy caused by a combination of two rare and de novo heterozygous variants in CACNA1A and CELSR2, respectively. Polygenic mutation flies were established and logistic regression were applied to study the gene–gene interaction and quantify the seizure‐risk weight of epilepsy‐associated genes in a polygenic background. In addition, calcium imaging, pharmacology, and transgenic rescue experiments were used to explore the mechanism and the precision medicine strategy for this model. Results Seizure‐like activity was mitigated in the Cacna1a ‐ Celsr2 digenic knockdown flies, whereas it was aggravated in the Cacna1a knockin‐ Celsr2 knockdown flies, and all relevant monogenic mutation flies showed seizures. Logistic regression suggested that the Cacna1a deficiency provided a protective effect against seizures in Celsr2 knockdown flies. The severe seizures from Cacna1a knockin‐ Celsr2 knockdown, the genotype mimicking that of the patient, can be completely rescued by inhibiting the calcium channel via genetic ( Cacna1a knockdown) or pharmacologic (pregabalin) treatment during a limited period of development. Calcium imaging results suggested a synaptic cleft balance mechanism for the protective effect of CACNA1A deficiency in the polygenic background. Significance CACNA1A presented multiple effects on epileptogenesis in diverse genetic backgrounds and provided an effective preclinical approach to clarify the net impact of polygenic variants for designing a precisive medicine strategy against refractory epilepsy.