Single-cell Transcriptomic Analysis of Cell Type Plasticity in Barrel Cortex of Normal and Autism Model Mice

项目总结 在被称为关键期(CPS)的出生后发育阶段，感觉经验作用于 基因硬连线连接图，以雕刻新皮质回路，使哺乳动物发挥功能。 神经发育障碍，如自闭症，会破坏这种依赖经验的可塑性和妥协 社交、认知和身体功能的发展。自闭症谱系障碍(ASD)患者 患有可能反映感觉回路异常发育的触觉高或低敏感性，ASD是 通常在初级躯体感觉皮质(S1)进行研究。此外，小鼠的胡须S1是体视性的 鼠标须垫图，因此操纵特定的胡须可以诱导可观察到的功能变化 相应的S1桶。人的经验依赖性可塑性的形态和生理研究 S1揭示了几种CPS，并阐明了ASD对它们在小鼠模型中出现的影响 自闭症。然而，依赖经验的可塑性和基因表达程序 在S1‘S 100+转录差异表达细胞的分辨下，ASD对其的影响尚不清楚 类型。由于这些细胞类型形成了执行感觉功能的回路，因此研究 经历和ASD对其成熟度的影响。该项目结合了单核mRNA测序 (SnRNA-seq)和计算生物学方法，植根于机器学习，具有时间分辨率 胡须操作和ASD的小鼠模型来验证两个假设。来检验胡须的假设 需要在S1中进行细胞类型开发的经验，将在几个时间点执行SnRNA-seq 跨越两个已建立的CP，在没有胡须的小鼠和对照组小鼠中。无人监督和有监督的机器 学习方法，如降维、聚类、图嵌入和分类 用于识别每个时间点的转录细胞类型，并评估胡须经验对 他们的成熟。杂交链反应荧光原位杂交(HCR-FISH)将使 确认特定细胞类型的发育模式。来检验ASD破坏的假说 依赖经验的细胞类型成熟，SnRNA-seq将在Fmr1 KO小鼠上根据晶须进行 剥夺和控制条件。FMR1 KO模型脆性X综合征，最常见的单基因原因 人类的智力残疾和自闭症。而Fmr1缺失已被证明延缓了成熟 在CP期间，它对S1细胞类型经验依赖性成熟的影响尚不清楚。 KO小鼠和野生型小鼠基因表达谱和细胞类型的比较 去除胡须将揭示ASD的转录特征，并确定其影响的细胞类型 都是本地化的。从这项研究中获得的关于ASD在转录转录细胞类型中的表现的知识 将提高对ASD病理的理解，并揭示靶向治疗的候选细胞类型。

PROJECT SUMMARY During postnatal developmental stages known as critical periods (CPs), sensory experience acts upon a genetically-hardwired connectivity map to sculpt the neocortical circuitry that enables mammalian functioning. Neurodevelopmental disorders such as autism disrupt this experience-dependent plasticity and compromise the development of social, cognitive, and physical function. Since autism spectrum disorder (ASD) patients suffer from tactile hyper- or hypo-sensitivity that may reflect abnormal development of sensory circuits, ASD is commonly studied in primary somatosensory cortex (S1). In addition, the mouse whisker S1 is a somatotopic map of the mouse whisker pad, so manipulation of specific whiskers induces observable functional changes in the corresponding barrels of S1. Morphological and physiological studies of experience-dependent plasticity in S1 have revealed several CPs and elucidated the influence of ASD on their emergence in mouse models of autism. However, the gene expression programs underlying experience-dependent plasticity and the influence of ASD on it remain unknown at the resolution of S1’s 100+ transcriptomically distinct cell types. Since these cell types form the circuits that carry out sensory function, it is important to study the influence of experience and ASD on their maturation. This project combines single-nucleus mRNA sequencing (snRNA-seq) and computational biology approaches rooted in machine learning with temporally resolved whisker manipulations and a mouse model of ASD to test two hypotheses. To test the hypothesis that whisker experience is required for cell type development in S1, snRNA-seq will be performed at several time points spanning two established CPs in whisker-deprived and control mice. Unsupervised and supervised machine learning approaches such as dimensionality reduction, clustering, graph embedding, and classification will be used to identify transcriptomic cell types at each time point and assess the influence of whisker experience on their maturation. Hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) will enable the validation of cell type-specific development patterns. To test the hypothesis that ASD disrupts experience-dependent cell type maturation, snRNA-seq will be performed on Fmr1 KO mice under whisker deprivation and control conditions. Fmr1 KO models Fragile X syndrome, the most frequent monogenic cause of intellectual disability and ASD in humans. While Fmr1 deletion has been shown to delay the maturation of circuits in S1 during a CP, its influence on experience-dependent maturation of S1 cell types remains unknown. Comparing gene expression profiles and cell types between KO and wild-type mice with and without whisker-deprivation will reveal transcriptomic signatures of ASD and pinpoint the cell types in which its effects are localized. Knowledge generated from this study about the manifestation of ASD in transcriptomic cell types will improve understanding of ASD pathology and reveal candidate cell types for targeted treatment.