Splicing variants in DEPDC5-related epilepsies: From functional characterization to correction

Area of Science:

• Genetics
• Molecular Biology
• Neurology

Background:

• Familial focal epilepsies are often linked to variants in genes of the GATOR1 complex, including DEPDC5.
• The impact of most identified DEPDC5 variants on gene splicing remains largely uncharacterized.
• Understanding splicing alterations is crucial for diagnosing and potentially treating DEPDC5-related epilepsies.

Purpose of the Study:

• To investigate the role of intronic and exonic splicing variants in the DEPDC5 gene in familial focal epilepsies.
• To analyze the functional impact of previously reported DEPDC5 variants on splicing.
• To develop a strategy for correcting DEPDC5 splicing defects.

Main Methods:

• Utilized gene panel, whole-exome sequencing (WES), and whole-genome sequencing (WGS) to identify DEPDC5 variants in familial epilepsy cases.
• Employed RNA analysis and minigene assays to assess the impact of variants on splicing.
• Developed a modified small nuclear RNA (snRNA) system to correct a specific splicing defect.

Main Results:

• Identified canonical splice-site, missense, and synonymous variants in DEPDC5, confirming pathogenicity and elucidating splicing disruption mechanisms.
• Found that 13.6% of reported DEPDC5 single nucleotide variants may affect splicing, with potential for misannotation in non-canonical intronic variants.
• Demonstrated diverse splicing alteration mechanisms, including cryptic splice site activation and enhancer disruption, and successfully corrected a patient variant using modified snRNAs.

Conclusions:

• This research deepens the understanding of DEPDC5 splicing variants in familial focal epilepsies.
• The development of an snRNA-based correction system offers a promising therapeutic avenue for DEPDC5-related epilepsy.
• This work establishes a foundation for personalized treatment strategies targeting genetic epilepsy subtypes.