The genetic origins of neuropsychiatric disorders lie in the developing brain, where cells undergo highly intricate and time-sensitive changes governed by gene regulation. One crucial mechanism, alternative splicing, allows individual genes to produce RNA isoforms of variable structures and functions. Although emerging evidence indicates neuropsychiatric disorder risk is more closely linked to dysregulation at the isoform level than the gene level, the expression profiles and functions of isoforms in the prenatal brain remain poorly understood.
To address this gap, we investigated the landscape and functional roles of isoforms during brain development. Using stem cell-derived neuron and brain organoid models, and targeted nanopore long-read sequencing, we characterized isoforms from seven neuropsychiatric risk genes across key developmental stages. We identified 313 isoforms, with novel isoforms accounting for 43% of total gene expression, indicating the developmental transcriptome is more complex than previously acknowledged. Notably, multiple novel isoforms of CACNA1C, KLC1, and RBFOX1, exhibited high usage and dynamic expression, suggesting isoform-specific roles in neurodevelopmental processes. For example, a novel RBFOX1 isoform was highly expressed in 3 month organoids dominated by excitatory neurons but downregulated at 6 months when glial cell-types emerge. Moreover, meta-analysis of neuropsychiatric risk QTL datasets identified risk-associated KLC1 isoforms, motivating further investigation into the functional consequences of altered splicing.
This study uncovers the molecular dynamics of brain development with isoform-level precision, illuminating how splicing governs neurodevelopmental processes and contributes to mental health disorder risk. Continued investigation into the biological roles of the risk-associated isoforms will be critical for revealing key drivers of neuropsychiatric pathogenesis and guide the development of future therapeutic targets.