Long-read CaptureSeq identifies novel RNA isoforms of psychiatric risk genes

Abstract

Alternative splicing is fundamental to brain development and physiology, and its disruption has been strongly associated with neurodevelopmental disorders (NDDs). NDD risk genes tend to be complex, having hundreds of currently annotated isoforms. However, these genes often have low to medium abundance in the brain. This causes a significant power loss in accurately quantifying isoforms and assessing their regulation through current transcriptome-wide sequencing approaches. To address this gap, we combine CaptureSeq target enrichment with sample barcoding and nanopore sequencing to characterise and quantify RNA isoform profiles of 1,221 protein-coding and lncRNA genes in human post-mortem tissue. We first demonstrate that our method preserves the quantitative aspect of transcript expression using synthetic spike-ins. We then profiled 52 prefrontal cortex, caudate, and hippocampus samples from 20 individuals (four adult and four fetal controls, and 12 adults with a neuropsychiatric diagnosis). We identified 44,624 unique isoforms, of which 88.4% were previously unannotated in GENCODE. Our analysis revealed 228 significant changes in isoform proportions (i.e. switches) between control adult brain regions, 257 between adult and fetal cortex, and 114 in genes between controls and individuals with a neuropsychiatric diagnosis, with some predicted to impact the coding potential and protein structure. For example, we identify a novel isoform of schizophrenia risk gene CPEB1 that constitutes 94% of the gene’s expression in schizophrenia cortex samples, suggesting that existing human brain annotations are far from complete. Our approach proves sensitive for cost-efficient investigations of isoform regulation across tissues, during development, or under different conditions.

Biography

Sofia Kudasheva is a third year PhD student working in the Haerty lab at the Earlham Institute, UK. Her research involves using long-read sequencing to identify novel isoforms and study alternative splicing in different biological contexts with a focus on the human brain.