Identifying Intrinsic Regulators of Areal Patterning in The Neocortex by Single-Cell RNA-seq and Organoid Arealization

识别新皮质区域模式的内在调节因子 通过单细胞RNAseq和有机体区域化 项目摘要/摘要 成熟的人类新皮质(NCX)是一个极其复杂的结构，它在功能上被组织成 专门的区域，在其细胞结构和与大脑其他部分的连接模式方面是独特的。大脑皮层 这些区域选择性地专注于不同的过程，从认知和感觉到运动 输出。所有的新皮质兴奋性神经元(ExN)都来自共同的放射状胶质细胞祖细胞池，即 NCX的神经干细胞及其转运放大的中间祖细胞(IPC)。新生儿外来者 然后沿着RG支架迁移到皮质板，这一过程跨越了预期的区域。 然而，成熟的NCX是EXN群体的镶嵌。目前公认的是，NCX区域化是 内在遗传机制组合的结果，包括转录因子(TF)的差异 由祖细胞表达，以及外部影响，主要以丘脑皮质输入的形式表达。相对的 然而，这两个组成部分的贡献还没有被很好地理解。在过去的30年里，开创性的 研究发现了不同皮质区域的分子差异，以及对区域至关重要的基因。 规范，但仍有许多需要解释的地方。单细胞测序的最新进展 开始阐明存在于小鼠和人脑中的额外细胞类型多样性，具有显著的 其他相应的EXN亚型之间的转录区域差异。了解这些功能是如何 差异的出现对于了解神经发育障碍是如何发生的以及 更准确地模拟人类皮质细胞类型，并了解干细胞疗法如何最好地 以特定地区的方式发展。RG和ExN在以下地区的系统表征 开发NCX是研究内在区域化因素的有力途径。为此，我们以前已经 生成了包含约550,000个来自不同区域的单细胞转录组图谱的空间注记数据集 神经发生高峰期NCX的亚解剖。我的分析将集中在确定 NCX发育区特异的RG和ExN分子亚型，并确定其 独特的遗传标记和表达签名，特别强调TF。使用皮质 有机物，我将评估前面描述的关键区域化基因在 人类的背景。在这个系统的基础上，我将评估2个TF实现的功能重要性 在我的初步分析中发现，额叶和枕叶NCX的RG优先表达， 分别进行了分析。通过这项工作，我的目标是进一步阐明形成多样性的内在机制 穿过人类大脑皮层的各个区域。

Identifying Intrinsic Regulators Of Areal Patterning In The Neocortex by Single-Cell RNAseq And Organoid Arealization Project Summary/Abstract The mature human neocortex (Ncx) is an incredibly complex structure, which is organized into functionally specialized areas, unique in their cytoarchitecture and connectivity patterns to the rest of the brain. Cortical areas are selectively dedicated to distinct processes, ranging from cognition and sensory perception to motor output. All neocortical excitatory neurons (ExNs) arise from a common progenitor pool of radial glia (RG), the neural stem cells of the Ncx, and their transit-amplifying intermediate progenitor cells (IPCs). Newborn ExNs then migrate to the cortical plate along the RG scaffold, in a process conserved across prospective areas. However, the mature Ncx is a mosaic of ExN populations. It is currently accepted that Ncx arealization is the result of a combination of intrinsic genetic mechanisms, including transcription factors (TFs) differentially expressed by progenitors, and of extrinsic influences, primarily in the form of thalamocortical input. The relative contribution of these two components, however, is not well understood. Over the past 30 years, seminal studies have uncovered molecular differences across cortical areas, as well as genes crucial for areal specification, but still there remains much to be explained. Recent advances in single-cell sequencing have begun to illuminate additional cell type diversity that exists in mouse and human brains, with significant transcriptional areal differences between otherwise corresponding ExN subtypes. Understanding how these differences emerge is essential to understanding how neurodevelopmental disorders may arise, as well as to more accurately model human cortical cell types and understand how stem cell therapies may best be developed in an area specific manner. A systematic characterization of RG and ExNs across areas of the developing Ncx is a powerful approach to study intrinsic arealization factors. To this end, we have previously generated a spatially-annotated dataset of ~550,000 single-cell transcriptome profiles from distinct areal subdissections of the Ncx during the period of peak neurogenesis. My analysis will focus on identifying molecular subtypes of RG and ExNs specific to prospective areas of the developing Ncx, and determining their unique genetic markers and expression signatures, with a particular emphasis on TFs. Using cortical organoids, I will evaluate the capacity previously described key arealization genes to drive spatial identity in a human context. Building on this system, I will evaluate the functional importance for arealization of 2 TFs identified in my preliminary analyses as being preferentially expressed by RG of frontal and occipital Ncx, respectively. Through this work, I aim to further shed light on the intrinsic mechanisms that shape diversity across areas of the human neocortex.