Oral Presentation Australasian RNA Biology and Biotechnology Association 2024 Conference

Unveiling hidden neuropsychiatric risk gene isoforms in human brain with nanopore sequencing (108374)

Ricardo De Paoli-Iseppi 1 , Shweta Joshi 1 , Josie Gleeson 1 , Yair DJ Prawer 1 , Yupei You 1 2 , Ria Agarwal 1 , Anran Li 1 , Anthea Hull 1 , Rhea Kujawa 1 , Mriga Dutt 1 , Catriona McLean 3 4 , Benjamin Parker 1 , Michael Clark 1
  1. University of Melbourne, Parkville, VIC, Australia
  2. The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
  3. Victorian Brain Bank, The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
  4. Department of Anatomical Pathology, Alfred Health, Melbourne, VIC, Australia

Normal brain development is contingent on precise spatial and temporal control over several layers of regulation. Alternative splicing of pre-mRNA is enriched in brain and is a key component of this regulation and its disruption has been associated with human disease including neuropsychiatric disorders [1, 2]. Recent genome-wide association studies have identified hundreds of risk loci for neuropsychiatric disorders [3]. Often located in noncoding areas, how these loci contribute to disease risk is not well understood. Recent evidence suggests that risk loci may contribute to disorder risk by disrupting alternative pre-mRNA splicing of risk genes, however most risk gene isoform profiles remain unknown [4].

Using Nanopore long-read sequencing we mapped the RNA isoform profiles of 31 neuropsychiatric risk genes. High-confidence risk gene mRNAs were sequenced on seven post-mortem human brain regions from five control individuals. Our bioinformatics pipelines IsoLamp and IsoVis were used to identify and annotate known and novel isoforms. In total, we identified 363 uncharacterised isoforms and 28 novel exons. We also find highly expressed novel isoforms in the schizophrenia (SCZ) risk genes ATG13 and CSMD1 for which these isoforms accounted for >50% of expression. Tissue specific expression of novel isoforms was identified including within the caudate for the SCZ risk gene DOC2A and cerebellum for the depression risk gene DCC. Mass spectrophotometry of brain protein isolates also confirmed translation of a novel exon skipping event in the SCZ risk gene ITIH4, suggesting a new regulatory mechanism for this gene.

Our results show current gene transcript annotations are incomplete and support the use of long-read sequencing to identify novel isoforms and exons in human brain. Uncovering the splicing repertoire for neuropsychiatric risk genes will help identify pathogenic isoforms, predict their function and potentially reveal new therapeutic pathways.

  1. Glinos, D.A., et al., Transcriptome variation in human tissues revealed by long-read sequencing. Nature, 2022. 608(7922): p. 353-359.
  2. Yeo, G., et al., Variation in alternative splicing across human tissues. Genome biology, 2004. 5(10): p. 1-15.
  3. Ripke, S., et al., Biological insights from 108 schizophrenia-associated genetic loci. Nature, 2014. 511(7510): p. 421.
  4. 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.