美国波士顿儿童医院Christopher A. Walsh团队的研究显示，空间转录组学揭示了人类皮质层和区域规格。该项研究成果发表在2025年5月14日出版的《自然》上。

在这里，课题组利用基于深度学习的核核分割技术，结合多路错误-机器人荧光原位杂交技术（MERFISH），利用空间分辨的单细胞分辨率来研究人类胎儿皮质的分子、细胞和细胞结构发育。他们广泛的空间地图集，包含超过18个一百万个单细胞，跨越七个发育时间点的八个皮质区域。该团队发现了早期建立的六层结构，通过兴奋性神经元亚型的层流分布来识别，在细胞结构层出现前的几个月。

值得注意的是，课题组研究人员在妊娠中期发现了两种截然不同的皮质区域划分模式：(1)沿着前后轴观察到大多数皮质区域连续渐进的过渡；(2)早在妊娠周就在主要（V1）和次要（V2）视觉皮质之间明确地确定了一个离散的、突然的边界。这种V1-V2神经元亚型的尖锐二元转变挑战了妊娠中期皮层形成只涉及梯度样转变的观念。

此外，将单核RNA测序与MERFISH结合，揭示了v1特异性层突触发生的早期上调4神经元。总的来说，他们的发现强调了空间关系在决定皮层层和区域的分子特征方面的关键作用。本研究建立了一种空间分辨的单细胞分析范式，为构建全面的人类大脑发育图谱铺平了道路。

据介绍，人类大脑皮层由六层和几十个在分子和结构上都不同的区域组成。尽管单细胞转录组学研究已经推进了人类皮质发育的分子表征，但由于细胞分离过程中空间背景的缺失，存在着实质性的空白。

附：英文原文

Title: Spatial transcriptomics reveals human cortical layer and area specification

Author: Qian, Xuyu, Coleman, Kyle, Jiang, Shunzhou, Kriz, Andrea J., Marciano, Jack H., Luo, Chunyu, Cai, Chunhui, Manam, Monica Devi, Caglayan, Emre, Lai, Abbe, Exposito-Alonso, David, Otani, Aoi, Ghosh, Urmi, Shao, Diane D., Andersen, Rebecca E., Neil, Jennifer E., Johnson, Robert, LeFevre, Alexandra, Hecht, Jonathan L., Micali, Nicola, Sestan, Nenad, Rakic, Pasko, Miller, Michael B., Sun, Liang, Stringer, Carsen, Li, Mingyao, Walsh, Christopher A.

Issue&Volume: 2025-05-14

Abstract: The human cerebral cortex is composed of six layers and dozens of areas that are molecularly and structurally distinct1,2,3,4. Although single-cell transcriptomic studies have advanced the molecular characterization of human cortical development, a substantial gap exists owing to the loss of spatial context during cell dissociation5,6,7,8. Here we used multiplexed error-robust fluorescence in situ hybridization (MERFISH)9, augmented with deep-learning-based nucleus segmentation, to examine the molecular, cellular and cytoarchitectural development of the human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing more than 18million single cells, spans eight cortical areas across seven developmental time points. We uncovered the early establishment of the six-layer structure, identifiable by the laminar distribution of excitatory neuron subtypes, 3months before the emergence of cytoarchitectural layers. Notably, we discovered two distinct modes of cortical areal specification during mid-gestation: (1) a continuous, gradual transition observed across most cortical areas along the anterior–posterior axis and (2) a discrete, abrupt boundary specifically identified between the primary (V1) and secondary (V2) visual cortices as early as gestational week20. This sharp binary transition in V1–V2 neuronal subtypes challenges the notion that mid-gestation cortical arealization involves only gradient-like transitions6,10. Furthermore, integrating single-nucleus RNA sequencing with MERFISH revealed an early upregulation of synaptogenesis in V1-specific layer4 neurons. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This study establishes a spatially resolved single-cell analysis paradigm and paves the way for the construction of a comprehensive developmental atlas of the human brain.

DOI: 10.1038/s41586-025-09010-1

Source: https://www.nature.com/articles/s41586-025-09010-1