Single-nuclei transcriptomics enable detection of somatic variants in patient brain tissue

Area of Science:

• Neuroscience
• Genetics
• Molecular Biology

Background:

• Somatic variants contribute to human diseases, including focal epilepsies, but their mosaic nature complicates study.
• Single-cell genomic and transcriptomic data coupling offers potential insights into variant roles in disease.

Purpose of the Study:

• To assess if single-nucleus 3'- or 5'-RNA sequencing can yield genotype data for known variants near transcript ends.
• To evaluate the utility of these methods for studying somatic variants in neurological disorders.

Main Methods:

• Comparison of commercially available single-nucleus 3'- and 5'-RNA sequencing kits.
• Analysis of resected brain samples from three pediatric focal epilepsy patients.
• Quantification of variant detection based on proximity to transcript ends.

Main Results:

• Single-nucleus RNA sequencing effectively detects known somatic variants when they are near transcript ends.
• The study demonstrated successful identification of cell types affected by a RHEB somatic variant in an epilepsy-associated cortical malformation.
• Performance varied based on the distance of the variant from the transcript end.

Conclusions:

• Single-nucleus 3'- or 5'-RNA sequencing is a viable approach for identifying somatic variants in single cells.
• This technique can help elucidate the cellular and molecular mechanisms underlying somatic variant-driven diseases like focal epilepsy.