Characterising the transcriptional profile of the calcium channel gene CACNA1F in human brain

Introduction

• Voltage-gated calcium channels (VGCCs) significantly affect many aspects of brain function including neuronal excitability and synaptic plasticity.
• Large-scale genetic studies implicate VGCCs in the pathophysiology of psychiatric disorders
• Each VGCC gene encodes multiple functionally-distinct isoforms via transcriptional mechanisms
• Brain-enriched VGCC isoforms might represent attractive therapeutic targets for psychiatric disorders, but the complement of VGCC isoforms present in human tissues, including brain, remains largely unknown
• The CACNA1F gene encodes Ca_V1.4 which has been associated with educational attainment. It is not reported to be expressed in brain tissue but there is little direct investigation of this possibility in humans
• We investigated whether there is evidence of expression at the CACNA1F locus in publicly-available brain RNASeq data produced by the Lieber Institute for Brain Development (LIBD)
• The LIBD data indicated the possible presence of a truncated isoform of CACNA1F in human postmortem dorsolateral prefrontal cortex

Methods

• RNA from 8 brain regions of 6 healthy controls was reverse transcribed to examine expression of truncated CACNA1F in human brain
• Primers were designed to target both the full-length CACNA1F and truncated CACNA1F mRNA, based on the LIBD RNASeq data
• We were able to amplify truncated, but not full length, CACNA1F
• Nanopore long-read sequencing was used to examine the diversity of truncated CACNA1F isoforms (see right), using a novel bioinformatics pipeline

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