Charting the spatial transcriptome of the human cerebral cortex at single-cell resolution

Songren Wei, Meng Luo, Pingping Wang, Rui Chen, Xiyun Jin, Chang Xu, Chenyang Li, Xiaoyu Lin, Zhaochun Xu, Hongxin Liu, Rui Cheng, Wenyi Yang, Yideng Cai, Guangfu Xue, Peng Huang, Zhigang Liu, Haoxiu Sun (), Jiangping Xu () and Qinghua Jiang ()
Additional contact information
Songren Wei: Harbin Medical University
Meng Luo: Harbin Institute of Technology
Pingping Wang: Harbin Medical University
Rui Chen: Guangdong Medical University
Xiyun Jin: Harbin Institute of Technology
Chang Xu: Harbin Institute of Technology
Chenyang Li: Guangdong-Hong Kong-Macao Greater Bay Area
Xiaoyu Lin: Harbin Institute of Technology
Zhaochun Xu: Harbin Institute of Technology
Hongxin Liu: Harbin Institute of Technology
Rui Cheng: Harbin Institute of Technology
Wenyi Yang: Harbin Institute of Technology
Yideng Cai: Harbin Institute of Technology
Guangfu Xue: Harbin Institute of Technology
Peng Huang: Southern Medical University
Zhigang Liu: Southern Medical University
Haoxiu Sun: Harbin Medical University
Jiangping Xu: Southern Medical University
Qinghua Jiang: Harbin Medical University

Nature Communications, 2025, vol. 16, issue 1, 1-20

Abstract: Abstract A high-resolution spatial physiological atlas of cortical neurons serves as an essential reference for studying neurological diseases and is crucial for a comprehensive understanding of the cortical functions and physiological mechanisms. Although previous studies have elucidated the cellular basis of individual cortex, the molecular characteristics and precise spatial organization of neural cells within multiple human cortex remain incompletely understood. Subcellular-level spatial transcriptomic sequencing and snRNA-seq enabled mapping of 14 human cortical regions, creating a single-cell atlas with transcriptomic data from 1,121,772 nuclei and spatial profiles from 1,888,306 cells to characterize neural cell organization. The atlas reveals distinct expression patterns and spatial arrangements of neural cell types. Glutamatergic neurons show precise laminar patterns, with similar expression in adjacent cortex. SST neurons fall into two transcriptional categories, corresponding to superficial and deep layer distributions. The atlas, integrated with functional networks, highlights correlations between neural cell types and cortical functions, uncovering cell-cell interactions and ligand-receptor patterns with regional differences in neuron-glia communication. It also deciphers transcriptomic differences and cellular composition in layer 4 and the stable subplate (layer 6b) across regions. Our findings offer insights into the cellular foundations of complex and intelligent regions within the human cortex.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-62793-9 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62793-9

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-62793-9

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().