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

正常和自闭症模型小鼠桶状皮层细胞类型可塑性的单细胞转录组分析

• 批准号: 10750812
• 负责人: Salwan Butrus
• 金额: $ 4.38万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10750812
• 关键词: ASD patient; Anatomy; Brain; Cell Nucleus; Cells; Classification; Computational Biology; Development; Dimensions; Disease; Disease model; Electrophysiology (science); Embryo; Endowment; FMR1; Fluorescent in Situ Hybridization; Fragile X Syndrome; Functional disorder; Gene Expression; Genes; Glutamates; Graph; Health; Heterogeneity; Histology; Human; Impairment; Intellectual functioning disability; Knock-out; Knockout Mice; Knowledge; Life; Machine Learning; Maps; Measurement; Modeling; Molecular; Morphology; Mus; Neocortex; Neurodevelopmental Disorder; Neurons; Pathology; Pattern; Physical Function; Physiological; Reaction; Resolution; Resources; Role; Sensorimotor functions; Sensory; Sensory Deprivation; Series; Social Development; Social Functioning; Somatosensory Cortex; Specific qualifier value; Stereotyping; Structure; Synapses; Tactile; Testing; Therapeutic Intervention; Time; Tissues; Transgenic Mice; Validation; Vibrissae; Vision; Visual; Wild Type Mouse; Work; area striata; autism spectrum disorder; barrel cortex; cell type; cognitive function; critical period; deprivation; differential expression; experience; experimental study; improved; mRNA sequencing; machine learning pipeline; mouse model; neocortical; neural circuit; postnatal; postnatal development; programs; response; sensory cortex; single nucleus RNA-sequencing; somatosensory; supervised learning; synaptogenesis; targeted treatment; temporal measurement; transcriptomics; unsupervised learning

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.

项目摘要 在产后发育阶段被称为关键时期（CPS），感官经验作用于 基因连接图雕刻的新皮层电路，以实现哺乳动物的功能。 自闭症等神经发育障碍破坏了这种依赖经验的可塑性和妥协 社会，认知和身体机能的发展。由于自闭症谱系障碍（ASD）患者 遭受触觉过度或低敏感性，可能反映了感觉电路异常发育，ASD是 通常在原发性体感皮质（S1）中进行研究。此外，小鼠晶须S1是体体 小鼠晶须垫的地图，因此操纵特定晶须会引起可观察到的功能变化 S1的相应桶。经验依赖性可塑性的形态学和物理研究 S1揭示了几个CP，并阐明了ASD对它们在小鼠模型中出现的影响 自闭症。但是，基因表达程序是基于经验依赖性可塑性和 在S1的100+转录不同细胞的分辨率下，ASD对其对其的影响仍然未知 类型。由于这些细胞类型形成了执行感官功能的电路，因此研究 经验和ASD对成熟的影响。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，并暂时解决 晶须操纵和ASD小鼠模型检验两个假设。测试晶须的假设 S1中的细胞类型开发需要经验，将在几个时间点进行SNRNA-SEQ 跨越两个在晶须剥落和控制小鼠中建立的CP。无监督和监督的机器 诸如降低维度，聚类，图形嵌入和分类之类的学习方法将是 用于在每个时间点识别转录组细胞类型，并评估晶须体验的影响 他们的成熟。杂交链反应荧光原位杂交（HCR-FISH）将使 验证细胞类型特异性开发模式。测试ASD破坏的假设 依赖经验的细胞类型成熟，SNRNA-SEQ将在晶须下进行FMR1 KO小鼠进行 剥夺和控制条件。 FMR1 KO模型脆弱的X综合征，最常见的单基因原因 人类的智力残疾和ASD。虽然已显示FMR1删除已延迟成熟 CP期间S1中的电路对S1细胞类型的经验依赖性成熟的影响仍然未知。 比较有或没有的KO和野生型小鼠之间的基因表达谱和细胞类型 晶须剥夺将揭示ASD的转录组特征，并查明其效果的细胞类型 是本地化的。这项研究对转录组细胞类型中ASD的表现产生的知识 将提高对ASD病理学的理解，并揭示针对靶向治疗的候选细胞类型。