Single-cell spatiotemporal transcriptome dynamics of mouse prefrontal cortex intratelencephalic neurons during postnatal development

The prefrontal cortex (PFC) is a core regulatory center for higher cognitive functions in the mammalian brain. In early postnatal mice, the PFC remains incompletely mature, particularly the intratelencephalic (IT) neurons located in superficial layers. However, the molecular developmental trajectories and regulatory mechanisms of IT neurons during the critical postnatal period (1-2 weeks) for circuit establishment, remain poorly characterized at single-cell resolution. Here, we performed single-cell RNA sequencing analysis on mouse PFC isolated at different developmental time points, and integrated with spatial transcriptomic data. Our study systematically deciphered the spatiotemporal transcriptome dynamics of mouse PFC during postnatal development, with particular emphasis on the heterogeneity of IT neurons. We identified dynamically expressed genes during postnatal development, including cadherin and axon guidance molecule genes, as well as specific transcriptional regulators that control the maturation of IT neurons in different layers. Furthermore, we also revealed that glial cells play crucial regulatory roles in IT neuron development through specific signaling pathways. Our study provides a comprehensive single-cell atlas of postnatal mouse PFC development, offering important insights into the mechanisms of neural development and circuit assembly in PFC. To delineate the molecular trajectories underlying postnatal development of prefrontal cortex (PFC) neurons and investigate the mechanisms governing early neural circuit assembly, we performed high-throughput single-cell RNA sequencing (scRNA-seq) on PFC tissues from mice across key developmental timepoints (postnatal day: P1, P4, P10 and adulthood: P84). Our comprehensive transcriptomic atlas captured dynamic gene expression patterns during critical stages of neuronal maturation.前额叶皮层（prefrontal cortex, PFC）是哺乳动物大脑中调控高级认知功能的核心中枢。在出生后早期的小鼠中，PFC尚未完全成熟，尤其是位于皮层浅表层的端脑内投射神经元（intratelencephalic, IT）。然而，在环路构建关键的出生后早期（1~2周）阶段，IT神经元的分子发育轨迹及调控机制在单细胞分辨率下仍未得到充分解析。本研究针对不同发育时间点分离的小鼠PFC组织开展单细胞RNA测序分析，并整合空间转录组数据。本研究系统解析了小鼠PFC出生后发育过程中的时空转录组动态变化，重点聚焦IT神经元的异质性。本研究鉴定出出生后发育过程中的动态表达基因，包括钙粘蛋白家族基因、轴突导向分子基因，以及调控不同皮层层IT神经元成熟的特异性转录调控因子。此外，本研究还揭示了胶质细胞通过特定信号通路在IT神经元发育过程中发挥关键调控作用。本研究构建了小鼠PFC出生后发育的完整单细胞图谱，为解析PFC的神经发育及环路组装机制提供了重要参考。为阐明前额叶皮层神经元出生后发育的分子轨迹并解析早期神经环路组装的调控机制，本研究对关键发育时间点（出生后第1天P1、第4天P4、第10天P10以及成年期P84）的小鼠PFC组织进行了高通量单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）。本研究构建的完整转录组图谱捕捉到了神经元成熟关键阶段的动态基因表达模式。