RNA-seq analysis of Scn1+/- Dravet mice on susceptible and resistant strains at postnatal days 14 and 24

Dravet syndrome is a severe, early-onset epileptic encephalopathy frequently resulting from de novo mutations of SCN1A. Mice with heterozygous deletion of Scn1a (Scn1a+/-) model many features of Dravet syndrome, including spontaneous seizures and premature lethality. Scn1a+/- mice exhibit variable phenotype penetrance and expressivity dependent upon the strain background. On the 129S6/SvEvTac (129) strain, Scn1a+/- mice do not display an overt phenotype. However Scn1a+/- mice on the [129S6xB6]F1 strain (F1.Scn1a+/-) exhibit juvenile-onset spontaneous seizures and premature lethality. QTL mapping identified several modifier loci responsible for strain-dependent differences in survival of Scn1a+/- mice, but these loci do not account for all the observed phenotypic variance. Global RNA-seq analysis was performed to identify additional genes and pathways that may contribute to variable phenotypes. Hippocampal gene expression was analyzed in wild-type (WT) and Scn1a+/- mice on both F1 and 129 strains, at two time points during disease development. There were few gene expression differences between 129.WT and 129. Scn1a+/- mice and approximately 100 genes with small expression differences (6-36%) between F1.WT and F1.Scn1a+/- mice. Strain-specific gene expression differences were more pronounced, with dozens of genes with >1.5-fold expression differences between 129 and F1 strains. Age-specific and seizure-related gene expression differences were most prominent, with hundreds of genes with >2-fold differences in expression were identified between groups with and without seizures, suggesting potential differences in developmental trajectory and/or homeostatic plasticity during disease onset. Global expression differences in the context of Scn1a deletion may account for strain-dependent variation in seizure susceptibility and survival observed in Scn1a+/- mice. Hippocampal mRNA expression profiles of P14 and P24 wild-type and Scn1a+/- mice were generated by deep sequencing of 2-3 replicates using Illumina HiSeq4000德雷维特综合征（Dravet syndrome）是一种重症早发性癫痫性脑病，其致病原因多为SCN1A基因的新生突变。Scn1a基因杂合缺失（Scn1a+/-）小鼠可复现德雷维特综合征的多种核心表型，包括自发性癫痫发作与过早死亡。Scn1a+/-小鼠的表型外显率与表现度存在显著差异，且依赖于小鼠品系背景：在129S6/SvEvTac（129）品系中，Scn1a+/-小鼠无明显异常表型；而在[129S6xB6]F1杂交品系（F1.Scn1a+/-）中，该类小鼠则表现出幼年起病的自发性癫痫发作与过早死亡表型。 此前的数量性状位点（QTL）定位已鉴定出多个可调控Scn1a+/-小鼠品系依赖型生存差异的修饰位点，但上述位点无法解释全部观测到的表型变异。为筛选参与表型异质性的其他基因与通路，本研究开展了全局RNA测序（RNA-seq）分析：在疾病进展的两个时间点，对F1与129品系的野生型（WT）及Scn1a+/-小鼠的海马基因表达水平进行了检测。 结果显示，129品系的WT与Scn1a+/-小鼠之间基因表达差异极小；而F1品系的WT与F1.Scn1a+/-小鼠间则有约100个基因存在6%~36%的轻度表达差异。品系特异性的基因表达差异更为显著：129与F1品系间存在数十个基因的表达差异倍数超过1.5。年龄特异性及与癫痫发作相关的基因表达差异最为突出：在伴与不伴癫痫发作的小鼠组中，共鉴定出数百个表达差异倍数超过2的基因，这提示疾病发作阶段的发育轨迹和/或内稳态可塑性可能存在差异。 Scn1a基因缺失背景下的全局表达差异，或可解释Scn1a+/-小鼠中观测到的、品系依赖的癫痫易感性与生存差异。本研究通过Illumina HiSeq4000平台对2~3个生物学重复进行深度测序，获取了出生后第14天（P14）与出生后第24天（P24）龄野生型及Scn1a+/-小鼠的海马mRNA表达谱。