Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain

Lindsay Liang,Donna M Werling,Sirisha Pochareddy,Nenad Sestan,Joon-Yong An,John L R Rubenstein,Siavash Fazel Darbandi,Brooke K Sheppard,Stephan J Sanders,Michael C Gilson,Kevin J Bender,Forrest O Gulden,Atehsa Sahagun

doi:10.1186/s13073-021-00949-0

Abstract

BackgroundGenetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, and autism spectrum disorder. The mRNA splicing patterns of all four genes vary across development in the rodent brain, including mutually exclusive copies of the fifth protein-coding exon detected in the neonate (5N) and adult (5A). A second pair of mutually exclusive exons is reported in SCN8A only (18N and 18A). We aimed to quantify the expression of individual exons in the developing human brain.MethodsRNA-seq data from 783 human brain samples across development were analyzed to estimate exon-level expression. Developmental changes in exon utilization were validated by assessing intron splicing. Exon expression was also estimated in RNA-seq data from 58 developing mouse neocortical samples.ResultsIn the mature human neocortex, exon 5A is consistently expressed at least 4-fold higher than exon 5N in all four genes. For SCN2A, SCN3A, and SCN8A, a brain-wide synchronized 5N to 5A transition occurs between 24 post-conceptual weeks (2nd trimester) and 6 years of age. In mice, the equivalent 5N to 5A transition begins at or before embryonic day 15.5. In SCN8A, over 90% of transcripts in the mature human cortex include exon 18A. Early in fetal development, most transcripts include 18N or skip both 18N and 18A, with a transition to 18A inclusion occurring from 13 post-conceptual weeks to 6 months of age. No other protein-coding exons showed comparably dynamic developmental trajectories.ConclusionsExon usage in SCN1A, SCN2A, SCN3A, and SCN8A changes dramatically during human brain development. These splice isoforms, which alter the biophysical properties of the encoded channels, may account for some of the observed phenotypic differences across development and between specific variants. Manipulation of the proportion of splicing isoforms at appropriate stages of development may act as a therapeutic strategy for specific mutations or even epilepsy in general.

Highlights

Genetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, and autism spectrum disorder
Genetic variation in the genes SCN1A, SCN2A, SCN3A, and SCN8A are a major cause of epileptic encephalopathy, autism spectrum disorder (ASD), and developmental delay [1,2,3]
Expression of voltage-gated sodium channels in the human cortex Gene expression varies dramatically across development for many genes, especially during the late-fetal transition, during which half the genes expressed in the brain undergo a concerted increase or decrease in expression [12, 33, 34, 45]

Summary

Introduction

Genetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, and autism spectrum disorder. Genetic variation in the genes SCN1A, SCN2A, SCN3A, and SCN8A are a major cause of epileptic encephalopathy, autism spectrum disorder (ASD), and developmental delay [1,2,3] These four homologous genes encode voltage-gated sodium channels (NaV1.1, NaV1.2, NaV1.3, and NaV1.6, respectively) that are critical for a range of functions in the central nervous system [4], including axonal action potential initiation and propagation [5, 6], dendritic excitability [7, 8], macroscopic anatomical development [9], and activity-dependent myelination [10]. “N” isoforms use the alternative copy of exon 5 (5N), with an asparagine residue (Asn/N) at position 7 of 30 in SCN1A, SCN2A, and SCN8A and a serine residue (Ser/S) in SCN3A Despite this relatively small change in protein structure, differential inclusion of 5A or 5N can have marked effects on channel function. These splice isoforms can alter channel electrophysiological characteristics [24, 27], the functional impacts of variants associated with seizure [24], neuronal excitability [28], response to antiepileptics [21, 22, 29], and seizure-susceptibility [28]

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