Identification of MACF1 as a causative gene of generalised epilepsy

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Background The microtubule actin crosslinking factor 1 (MACF1) gene encodes microtubule–microfilament cross-linking factor 1 that plays an essential role in the embryonic brain development. MACF1 variants were associated with lissencephaly-9 (LIS9). However, the MACF1-epilepsy relationship was unknown. Methods Trios-based whole-exome sequencing was performed on a cohort with generalised epilepsy from the China Epilepsy Gene 1.0 project. The spatial–temporal expression, single-cell sequencing and genotype–phenotype correlation were analysed to explore the role of MACF1 in epilepsy and neurodevelopment. Results Two de novo heterozygous and eight biallelic MACF1 variants were identified in 10 unrelated patients. The variants presented significantly high excess by multiple statistical analyses. All patients were diagnosed with generalised epilepsy, among whom three patients presented with neurodevelopmental delay. MACF1 was expressed throughout the lifespan, with three major peaks in the fetal, early childhood and adulthood stages, consistent with seizure onset ages of the patients. The highest expression in adulthood was in the thalamus nucleus, potentially associated with the pathogenesis of generalised epilepsy. The single-cell sequencing in organoids showed MACF1 is widely expressed in the developing brain, especially in the early stage, suggesting a vital role in neurodevelopment. Genotype–phenotype association analysis revealed that LIS9-associated variants were featured by de novo monoallelic variants clustered within the C-terminal; the autism spectrum disorder-associated variants were mainly de novo monoallelic variants located at the spectrin-repeat rod domains. In contrast, the epilepsy-associated variants were biallelic missense variants, and those in the plakin domain were potentially associated with neurodevelopment delay. Significance MACF1 is potentially a novel causative gene of generalised epilepsy.

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