Spatial transcriptomics reveals human cortical layer and area specification

• 成果类型: Article
• 署名作者: 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.
• 署名单位: Harvard University; Harvard Medical School; Harvard University Medical Affiliates; Boston Children's Hospital; Howard Hughes Medical Institute; Harvard University; Harvard Medical School; Harvard University Medical Affiliates; Boston Children's Hospital; University of Pennsylvania; Harvard University; Harvard University Medical Affiliates; Boston Children's Hospital; Harvard University; Harvard University Medical Affiliates; Boston Children's Hospital; Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; University System of Maryland; University of Maryland Baltimore; Harvard University; Harvard University Medical Affiliates; Beth Israel Deaconess Medical Center; Yale University; Yale University; Yale University; Yale University; Harvard University; Harvard Medical School; Harvard University Medical Affiliates; Brigham & Women's Hospital; Harvard University; Harvard University Medical Affiliates; Brigham & Women's Hospital; Howard Hughes Medical Institute; University of Pennsylvania; Harvard University; Harvard Medical School; Harvard University; Harvard Medical School
• 刊物名称: Nature
• ISSN/ISSBN: 0028-3407
• DOI: 10.1038/s41586-025-09010-1
• 发表日期: 2025-08-07
• 关键词: cerebral-cortex; human neocortex; human brain; cell-types; arealization; expression; monkey; atlas

摘要

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 18 million 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, 3 months 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 week 20. 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 layer 4 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.