Neuron-specific transcriptomic signatures indicate neuroinflammation and altered neuronal activity in ASD temporal cortex.

We present a comprehensive assessment of neuronal cell-type-specific gene expression and alternative splicing changes in ASD cortex, directly comparing RNA-seq results from bulk tissue with isolated neurons. We observe strong signatures of cell stress and neural-immune/inflammatory pathway activation present within ASD neurons—a signal that is typically attributed to astrocyte/microglial populations. Our findings also provide further evidence for the hypothesized imbalance of excitatory to inhibitory neuronal activity in the brains of individuals with ASD. Moreover, we find that the transcriptomic architecture of ASD interacts substantially with age, thus revealing windows of opportunity for treatments that target specific molecular pathology. Autism spectrum disorder (ASD) is a highly heterogeneous disorder, yet transcriptomic profiling of bulk brain tissue has identified substantial convergence among dysregulated genes and pathways in ASD. However, this approach lacks cell-specific resolution. We performed comprehensive transcriptomic analyses on bulk tissue and laser-capture microdissected (LCM) neurons from 59 postmortem human brains (27 ASD and 32 controls) in the superior temporal gyrus (STG) of individuals ranging from 2 to 73 years of age. In bulk tissue, synaptic signaling, heat shock protein-related pathways, and RNA splicing were significantly altered in ASD. There was age-dependent dysregulation of genes involved in gamma aminobutyric acid (GABA) (GAD1 and GAD2) and glutamate (SLC38A1) signaling pathways. In LCM neurons, AP-1-mediated neuroinflammation and insulin/IGF-1 signaling pathways were upregulated in ASD, while mitochondrial function, ribosome, and spliceosome components were downregulated. GABA synthesizing enzymes GAD1 and GAD2 were both downregulated in ASD neurons. Mechanistic modeling suggested a direct link between inflammation and ASD in neurons, and prioritized inflammation-associated genes for future study. Alterations in small nucleolar RNAs (snoRNAs) associated with splicing events suggested interplay between snoRNA dysregulation and splicing disruption in neurons of individuals with ASD. Our findings supported the fundamental hypothesis of altered neuronal communication in ASD, demonstrated that inflammation was elevated at least in part in ASD neurons, and may reveal windows of opportunity for biotherapeutics to target the trajectory of gene expression and clinical manifestation of ASD throughout the human lifespan.

我们对自闭症谱系障碍（ASD）皮质中神经元细胞类型特异性基因表达和可变剪接变化进行了全面评估，直接比较了来自大块组织和分离神经元的RNA测序结果。我们在ASD神经元中观察到细胞应激和神经 - 免疫/炎症通路激活的强烈特征——这种信号通常被归因于星形胶质细胞/小胶质细胞群体。我们的研究结果还为ASD个体大脑中兴奋性与抑制性神经元活动的假设性失衡提供了进一步证据。此外，我们发现ASD的转录组结构与年龄有显著相互作用，从而揭示了针对特定分子病理学治疗的机会窗口。 自闭症谱系障碍是一种高度异质性的疾病，然而对大块脑组织的转录组分析已经确定了ASD中失调基因和通路之间的大量趋同。然而，这种方法缺乏细胞特异性分辨率。我们对来自2至73岁个体的颞上回（STG）的59例死后人类大脑（27例ASD和32例对照）的大块组织和激光捕获显微切割（LCM）神经元进行了全面的转录组分析。在大块组织中，ASD中突触信号传导、热休克蛋白相关通路和RNA剪接发生了显著改变。参与γ - 氨基丁酸（GABA）（GAD1和GAD2）和谷氨酸（SLC38A1）信号通路的基因存在年龄依赖性失调。在LCM神经元中，AP - 1介导的神经炎症和胰岛素/IGF - 1信号通路在ASD中上调，而线粒体功能、核糖体和剪接体成分下调。GABA合成酶GAD1和GAD2在ASD神经元中均下调。机制建模表明神经元中炎症与ASD之间存在直接联系，并为未来研究确定了炎症相关基因的优先级。与剪接事件相关的小核仁RNA（snoRNAs）的改变表明ASD个体神经元中snoRNA失调和剪接破坏之间存在相互作用。我们的研究结果支持了ASD中神经元通讯改变的基本假设，证明了炎症至少在ASD神经元中部分升高，并且可能揭示了生物治疗针对人类整个生命周期中ASD基因表达轨迹和临床表现的机会窗口。