Targeting converging exons to treat autism spectrum disorders

Alternative splicing shows a unique profile in the brain and the dysregulation of alternative splicing networks has been repeatedly reported in autistic brains. While the causal mutations for autism spectrum disorders (ASD) are predominantly in synaptic genes or transcription regulators, mutations in multiple splicing regulators have been reported to be causal. These findings suggest splicing regulators function upstream of critical exons, and identifying such converging exons may nominate new druggable targets.

Cell-type-specific splicing is critical for human brain development, but identifying cell-type-specific transcripts remains challenging. In their Pilot Award project, Zhang and his team used single-cell RNA-Seq in combination with long-read sequencing (scIso-Seq) to identify cell-type-specific splice isoforms. Applied to cerebral organoids derived from human iPSC lines, they uncovered splicing events in ASD risk genes¹. The Pilot project established a platform to study cell-type-specific splicing defects caused by mutations in splicing regulators.

RNA-binding proteins (RBPs) such as splicing regulators are essential for gene regulation, and identifying their target RNAs across cell types will help to elucidate their regulatory and pathogenic mechanisms. Zhang’s team has developed PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing². They have benchmarked PIE-Seq and demonstrated its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Thus, PIE-Seq provides an orthogonal approach to identify cell-type-specific targets of splicing regulators.

This will allow them to determine whether causal splicing factors regulate shared targets. They will perform scIso-Seq to identify mutation-associated splice forms in human iPSC derived cerebral organoids. To validate the findings they will use PIE-Seq in the same system. In summary, this project may identify converging splice mechanisms underlying ASD pathogenesis and guide therapeutic target identification for future studies.

Reference

1. Yang Y. et al. Cell Rep. 42, 113335 (2023) PubMed