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

基本信息

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
项目类别：
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

项目摘要

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.

项目概要在称为关键期 (CP) 的出生后发育阶段，感官体验作用于基因硬连线连接图来塑造新皮质电路，使哺乳动物发挥功能。自闭症等神经发育障碍会破坏这种依赖于经验的可塑性和妥协自闭症谱系障碍 (ASD) 患者的社交、认知和身体功能的发展。患有触觉过敏或过敏症，这可能反映了感觉回路的异常发育，自闭症谱系障碍（ASD）是通常在初级体感皮层（S1）中进行研究此外，小鼠胡须 S1 是一种体感皮层。鼠标胡须垫的地图，因此对特定胡须的操纵会引起可观察到的功能变化 S1的相应桶的经验依赖性可塑性的形态学和生理学研究。 S1 揭示了几种 CP 并阐明了 ASD 对它们在小鼠模型中出现的影响然而，自闭症的基因表达程序是依赖于经验的可塑性和在 S1 的 100 多个转录组不同细胞的分辨率下，ASD 对其的影响仍然未知由于这些细胞类型形成执行感觉功能的电路，因此研究它们非常重要。该项目结合了单核 mRNA 测序。 (snRNA-seq) 和植根于具有时间解析的机器学习的计算生物学方法胡须操作和 ASD 小鼠模型来检验两个假设来检验胡须的假设。 S1 中的细胞类型开发需要经验，snRNA-seq 将在几个时间点进行跨越胡须剥夺小鼠和对照小鼠的两个既定 CP。降维、聚类、图嵌入和分类等学习方法将用于识别每个时间点的转录组细胞类型并评估胡须经验对转录组的影响它们的成熟将使杂交链式反应荧光原位杂交（HCR-FISH）成为可能。验证细胞类型特异性发育模式。检验自闭症谱系障碍 (ASD) 破坏的假设。经验依赖性细胞类型成熟，将在胡须下的 Fmr1 KO 小鼠上进行 snRNA-seq Fmr1 KO 模型的剥夺和控制条件是脆性 X 综合征，这是最常见的单基因原因。 Fmr1 缺失已被证明会延迟人类智力障碍和 ASD 的成熟。 CP 期间 S1 中的回路，其对 S1 细胞类型的经验依赖性成熟的影响仍然未知。比较 KO 和野生型小鼠之间的基因表达谱和细胞类型胡须剥夺将揭示 ASD 的转录组特征，并查明其影响的细胞类型本研究产生的有关转录组细胞类型中 ASD 表现的知识。将增进对 ASD 病理学的了解，并揭示用于靶向治疗的候选细胞类型。