Cell type-specific dysregulation of gene expression due to Chd8 loss of function during mouse cortical development [snRNA-seq]

Disruptive variants in the chromodomain helicase CHD8, which acts as a transcriptional regulator during neurodevelopment, are strongly associated with risk for autism spectrum disorder (ASD). Loss of CHD8 function is hypothesized to perturb gene regulatory networks in the developing brain, thereby contributing to ASD etiology. However, insight into the cell type-specific transcriptional effects of CHD8 loss of function remains limited. We used single-cell and single-nucleus RNA-sequencing to globally profile gene expression and identify dysregulated genes in the embryonic and juvenile wild type and Chd8+/ mouse cortex, respectively. Chd8 and other ASD risk-associated genes showed a convergent expression trajectory that was largely conserved between the mouse and human developing cortex, increasing from the progenitor zones to the cortical plate. Genes associated with risk for neurodevelopmental disorders and genes involved in neuron projection development, chromatin remodeling, signaling, and migration were dysregulated in Chd8+/ embryonic day (E) 12.5 radial glia. Genes implicated in synaptic organization and activity were dysregulated in Chd8+/ postnatal day (P) 25 deep- and upper-layer excitatory neurons, suggesting a delay in synaptic maturation or impaired synaptogenesis due to CHD8 loss of function. Our findings reveal a complex pattern of transcriptional dysregulation in Chd8+/ developing cortex, potentially with distinct biological impacts on progenitors and maturing neurons in the excitatory neuronal lineage. Single-nucleus RNA-seq (snRNA-seq) was performed on cortical tissue from postnatal day (P) 25 litter- and sex-matched pairs of wild type and Chd8+/- mice. Tissue from four pairs of mice was collected and processed individually染色质域解旋酶CHD8（chromodomain helicase CHD8）是神经发育过程中的转录调控因子，其功能破坏性变异与自闭症谱系障碍（ASD）的患病风险显著相关。现有假说认为，CHD8功能缺失会扰乱发育大脑中的基因调控网络，进而参与自闭症谱系障碍的致病过程。然而，目前对于CHD8功能缺失所引发的细胞类型特异性转录效应的认知仍较为有限。本研究分别采用单细胞RNA测序（single-cell RNA-sequencing）与单细胞核RNA测序（single-nucleus RNA-sequencing）技术，对野生型与Chd8+杂合小鼠的胚胎期大脑皮层（单细胞RNA测序）及幼年期大脑皮层（单细胞核RNA测序）进行基因表达全景分析，并筛选表达失调基因。CHD8与其他自闭症谱系障碍风险相关基因呈现出趋同的表达轨迹，该轨迹在小鼠与人类发育大脑皮层中高度保守，即从祖细胞区域向皮层板逐渐表达上调。在Chd8+杂合小鼠胚胎第12.5天（E12.5）的放射状胶质细胞中，与神经发育障碍风险相关的基因，以及参与神经元投射发育、染色质重塑、信号传导与细胞迁移的基因均出现表达失调。在Chd8+杂合小鼠出生后第25天（P25）的深层及浅层兴奋性神经元中，与突触组织及突触活动相关的基因出现表达失调，这提示CHD8功能缺失会导致突触成熟延迟或突触发生受损。本研究结果揭示了Chd8+杂合小鼠发育大脑皮层中复杂的转录失调模式，该模式可能对兴奋性神经元谱系中的祖细胞及成熟神经元产生截然不同的生物学影响。本研究对出生后第25天（P25）、同窝且性别匹配的野生型与Chd8+/-杂合小鼠的皮层组织进行了单细胞核RNA测序（snRNA-seq）。本研究共收集四组小鼠的皮层组织，并分别进行独立处理。