Poster Presentation 44th Lorne Genome Conference 2023

Discovery of novel neuropsychiatric disorder risk gene transcripts in human brain (#140)

Ricardo De Paoli-Iseppi 1 , Rhea M Kujawa 1 , Yoonji Seo 1 , Josie Gleeson 1 , Shweta S Joshi 1 , Michael B Clark 1
  1. University of Melbourne, Parkville, VIC, Australia

The brain has one of the highest levels of alternative splicing in human tissues, which contributes to expansive protein diversity and regulation. Aberrant splicing is associated with human diseases including neuropsychiatric disorders. Recently, genome-wide association studies have identified hundreds of genomic risk loci for neuropsychiatric disorders1,2. However, how these risk genes contribute to disease risk through altered gene expression and RNA splicing is not well understood3.

Leveraging the advantages of long-read Nanopore sequencing we reveal the precise RNA isoform profiles of 38 neuropsychiatric risk genes. High-confidence risk gene mRNAs were sequenced using seven post-mortem human brain regions from five healthy individuals. A custom informatics pipeline incorporating DiscoAnt and IsoMix was used to identify and annotate known and novel isoforms. We reveal highly expressed novel isoforms in the schizophrenia risk genes ATG13 and CPT1C and the depression risk gene SLC30A9. A moderately expressed isoform that includes a novel exon was identified in the autism risk gene XRN2. We also show brain region specific novel isoform expression in CPT1C and RBFOX1. To date, we have identified 302 novel isoforms and 9 novel exons. Using SQANTI4, 116 (38%) of these novel isoforms were classified as Novel Not In Catalog, indicating previously unknown splice donors/acceptors within the full coding sequence. Most novel exons (8/9) appear to be “poison exons”, which terminate translation and lead to RNA degradation, suggesting new regulatory mechanisms for these genes.

Our results show that current gene transcript annotations are incomplete and supports the use of long-read sequencing to identify novel isoforms and exons in human brain. Uncovering the splicing repertoire for neuropsychiatric risk genes will inform future assessment of the functional impact these isoforms have on neuropsychiatric disorder development.

  1. 1. Ripke, S., et al., Biological insights from 108 schizophrenia-associated genetic loci. Nature, 2014. 511(7510): p. 421.
  2. 2. Wang, Q., et al., A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data. Nature neuroscience, 2019. 22(5): p. 691.
  3. 3. Clark, M.B., et al., Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain. Molecular psychiatry, 2019: p. 1-11.
  4. 4. Tardaguila, M., et al., SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome research, 2018. 28(3): p. 396-411.