Developmental trajectories of thalamic nuclei revealed by single-cell transcriptome profiling and Shh perturbation

The thalamus is the principal information hub of the vertebrate brain, with essential roles in sensory and motor information processing, attention, and memory. The complex array of thalamic nuclei develops from a restricted pool of neural progenitors. We apply longitudinal single-cell RNA-sequencing and regional abrogation of Sonic hedgehog (Shh) to map the developmental trajectories of thalamic progenitors, intermediate progenitors, and post-mitotic neurons as they coalesce into distinct thalamic nuclei. These data reveal that the complex architecture of the thalamus is established early during embryonic brain development through the coordinated action of four cell differentiation lineages derived from Shh-dependent and independent progenitors. We systematically characterize the gene expression programs that define these thalamic lineages across time and demonstrate how their disruption upon Shh depletion causes pronounced locomotor impairment resembling infantile Parkinson's disease. These results reveal key principles of thalamic development and provide mechanistic insights into neurodevelopmental disorders resulting from thalamic dysfunction. Overall design: The thalamic primordia were micro-dissected from three embryos per control and SBE1/5 genotype according to anatomical landmarks at four developmental stages (E12.5, E14.5, E16.5, and E18.5) coinciding with peak periods of thalamic proliferation, neurogenesis, and differentiation (n=24 embryos in total).

丘脑（thalamus）是脊椎动物大脑的核心信息枢纽，在感觉与运动信息处理、注意力调控及记忆功能中发挥不可或缺的作用。丘脑核团的复杂结构起源于有限的神经祖细胞（neural progenitors）群体。本研究采用纵向单细胞RNA测序（longitudinal single-cell RNA-sequencing）技术，并结合音猬因子（Sonic hedgehog, Shh）的局部敲除实验，对丘脑祖细胞、中间祖细胞（intermediate progenitors）及有丝分裂后神经元（post-mitotic neurons）汇聚为不同丘脑核团的发育轨迹进行了系统绘制。
研究数据显示，丘脑的复杂架构在胚胎脑发育早期便已成型，其构建依赖于Shh依赖型与Shh非依赖型祖细胞所产生的四类细胞分化谱系的协同调控。本研究系统表征了随时间动态变化的、定义上述丘脑谱系的基因表达程序，并阐明了Shh缺失后这些谱系遭到破坏时，会引发类似婴儿型帕金森病的显著运动功能障碍。
本研究结果揭示了丘脑发育的核心规律，并为丘脑功能异常引发的神经发育障碍（neurodevelopmental disorders）提供了机制层面的深入解析。
实验设计概述：研究人员依据解剖学标志，在四个与丘脑增殖、神经发生及分化峰值阶段相符的发育时期（胚胎第12.5天、14.5天、16.5天及18.5天），分别从对照组与SBE1/5基因型胚胎中各显微解剖3枚丘脑原基，总计纳入24枚胚胎样本。