Variants of TSC1 are associated with developmental and epileptic encephalopathy and focal epilepsy without tuberous sclerosis : For the China Epilepsy Gene 1.0 Project

De novo heterozygous missense variants in ATP11A are associated with refractory focal epilepsy

BACKGROUND

ATP11A encodes an integral-membrane type IV P-type-adenosine triphosphatase that plays an important role in neural development by maintaining membrane lipid asymmetry. ATP11A de novo heterozygous missense variants have been reported to be associated with hypomyelinating leukodystrophy; however, the neurological symptoms of patients are often varying. In this study, we aimed to explore the relationship between ATP11A variants and epilepsy.

METHODS

Trio-based whole-exome sequencing was performed on patients with focal epilepsy. Multiple bioinformatics analyses were used to predict the pathogenicity of the variants. Previously reported literature was collected to analyse the relation between variants and phenotypes.

RESULTS

Two de novo heterozygous missense variants of ATP11A were identified in two unrelated patients with refractory focal epilepsy and were predicted to be pathogenic using multiple bioinformatics analyses. Then, six patients associated with missense variants were collected. Half of the patients (3/6) with variants located on/near the transmembrane regions (TMs) had more severe and multiple neurological symptoms, while the other half with non-TM variants had mild and single symptoms, indicating a correlation between variant location and phenotype. All patients showed progressively worsening conditions, potentially due to a gradually increased expression of ATP11A in the human brain over time.

CONCLUSION

This study suggested that de novo heterozygous missense variants of ATP11A are associated with refractory focal epilepsy. Missense variant-associated phenotypes range from epileptic seizures to severe neurological symptoms. It should be noted that patients with ATP11A variants have a gradually worsening potential.

De novo TANC2 variants caused developmental and epileptic encephalopathy and epilepsy

OBJECTIVE

The TANC2 gene encodes a scaffolding synaptic protein with essential roles in synaptic transmission. This study aims to explore the association between TANC2 and epilepsy and the mechanism underlying phenotypic variation.

METHODS

Trio-based exome sequencing was performed in patients with epilepsy from the China Epilepsy 1.0 cohort. The association between TANC2 and epilepsy was validated with a Drosophila model. The role of TANC2 in development was investigated by single-cell RNA sequencing in cerebral organoids and spatiotemporal expression across brain regions.

RESULTS

De novo TANC2 variants were identified in six unrelated cases, including four null and two missense variants. The six variants were classified as "pathogenic"/"likely pathogenic," according to the American College of Medical Genetics and Genomics guidelines. Patients with null variants exhibited severe phenotypes, including three with epilepsy and neurodevelopmental disorders (NDDs) and one with developmental and epileptic encephalopathy (DEE). In contrast, the patients with missense variants presented with only epilepsy. Genotype-phenotype correlation analysis revealed that variants associated with epilepsy and NDD were mostly null variants, whereas the missense variants were associated with NDD or epilepsy. NDD-associated missense variants exhibited more severe damage effects, compared with the epilepsy-associated missense variants. Functional studies in Drosophila suggested that knockdown TANC2 led to increased susceptibility to seizure-like behavior. TANC2 expresses highly in the brain, with three peaks in early fetal, infancy, and adulthood, coinciding with the onset ages of patients. Specifically, TANC2 exhibited the highest expression in the early fetal stage, indicating its vital role in early development. Single-cell RNA sequencing revealed an extensive expression of TANC2 in neurons in 1-month-old cerebral organoids, suggesting its vital role in neurodevelopment.

SIGNIFICANCE

This study suggested TANC2 as a causative gene of epilepsy and DEE. The phenotypic spectrums of TANC2 potentially ranged from early lethality, DEE, epilepsy with NDD, NDD, to mild epilepsy, depending on the damaging effects caused by variants.