Novel isoform identification in a neuropsychiatric disease gene

Bipoloar disorder and schizophrenia have a strong genetic component, with genome-wide association studies (GWAS) identifying many risk loci. One such locus, CACNA1C, which codes for a voltage-gated calcium channel subunit, is a potential therapeutic target; however, its extreme length (>13 kb), number of exons (>50), and high level of alternative splicing means that CACNA1C isoform structure and expression is poorly understood1.

Researchers from the University of Oxford and The Earlham Institute utilised nanopore sequencing to investigate CACNA1C expression in six regions of post-mortem human brain (cerebellum, striatum, and 4 cortical sub-regions)1. Long nanopore reads enabled the complete exonic structure of CACNA1C (6.5 kb) to be defined, allowing the identification of 38 putative novel exons and 90 isoforms2. Out of 40 previously annotated isoforms, only 7 were identified. The team suggests that one of the reasons for this discrepancy is the presence of false positives in the previous data, caused by the inherent complexities of assembling transcript sequences generated using alternative sequencing approaches.

Interestingly, 9 of the top 10 expressed isoforms were novel transcripts (Figure 1)2. Initial investigation of the 83 novel isoforms identified many that would alter the protein and its function. The team were also able to show that isoform profiles vary between brain regions and that the splicing of CACNA1C is more complex than currently appreciated2.

The lead researcher, Dr. Michael Clark, highlighted that: ‘These results are the first step in evaluating CACNA1C as a potential therapeutic target and demonstrate the power of long-read nanopore sequencing to elucidate the true nature of expressed genes’1.

Figure 9: Nine of the top ten most abundant CACNA1C isoforms identified in brain tissue were novel, highlighting the benefits of long reads for isoform characterisation. Image courtesy of Dr. Michael Clark, University of Oxford, UK.
  1. Clark, M. Elucidating the expression and splicing patterns of neuropsychiatric disease genes in human brain. Presentation.
  2. Clark, M.B. et al. Long-read sequencing reveals the splicing profile of the calcium channel gene CACNA1C in human brain. bioRxiv 260562 (2018).