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Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex
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Abstract
Elucidating the cellular organization of the cerebral cortex is critical for understanding brain structure and function. Using large-scale single-nucleus RNA sequencing and spatial transcriptomic analysis of 143 macaque cortical regions, we obtained a comprehensive atlas of 264 transcriptome-defined cortical cell types and mapped their spatial distribution across the entire cortex. We characterized the cortical layer and region preferences of glutamatergic, GABAergic, and non-neuronal cell types, as well as regional differences in cell-type composition and neighborhood complexity. Notably, we discovered a relationship between the regional distribution of various cell types and the region's hierarchical level in the visual and somatosensory systems. Cross-species comparison of transcriptomic data from human, macaque, and mouse cortices further revealed primate-specific cell types that are enriched in layer 4, with their marker genes expressed in a region-dependent manner. Our data provide a cellular and molecular basis for understanding the evolution, development, aging, and pathogenesis of the primate brain.
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Metadata
- Authors
- Chen, A., Sun, Y., Lei, Y., Li, C., Liao, S., Meng, J., Bai, Y., Liu, Z., Liang, Z., Zhu, Z., Yuan, N., Yang, H., Wu, Z., Lin, F., Wang, K., Li, M., Zhang, S., Yang, M., Fei, T., Zhuang, Z., Huang, Y., Zhang, Y., Xu, Y., Cui, L., Zhang, R., Han, L., Sun, X., Chen, B., Li, W., Huangfu, B., Ma, K., Ma, J., Li, Z., Lin, Y., Wang, H., Zhong, Y., Zhang, H., Yu, Q., Wang, Y., Liu, X., Peng, J., Liu, C., Chen, W., Pan, W., An, Y., Xia, S., Lu, Y., Wang, M., Song, X., Liu, S., Wang, Z., Gong, C., Huang, X., Yuan, Y., Zhao, Y., Chai, Q., Tan, X., Liu, J., Zheng, M., Li, S., Huang, Y., Hong, Y., Huang, Z., Li, M., Jin, M., Li, Y., Zhang, H., Sun, S., Gao, L., Bai, Y., Cheng, M., Hu, G., Liu, S., Wang, B., Xiang, B., Li, S., Li, H., Chen, M., Wang, S., Li, M., Liu, W., Liu, X., Zhao, Q., Lisby, M., Wang, J., Fang, J., Lin, Y., Xie, Q., Liu, Z., He, J., Xu, H., Huang, W., Mulder, J., Yang, H., Sun, Y., Uhlen, M., Poo, M., Wang, J., Yao, J., Wei, W., Li, Y., Shen, Z., Liu, L., Liu, Z., Xu, X., & Li, C.
- Affiliations
- BGI Group (China) (CN)
- Center for Excellence in Brain Science and Intelligence Technology (CN)
- Tencent (China) (CN)
- Shanghai Institute of Nutrition and Health (CN)
- China National GeneBank (CN)
- University of Copenhagen (DK)
- Science for Life Laboratory (SE)
- Chinese Academy of Sciences (CN)
- Corresponding author
- Sun, Yidi
- Yao, Jianhua
- Li, Yuxiang
- Shen, Zhiming
- Liu, Longqi
- Liu, Zhiyong
- Xu, Xun
- Li, Chengyu
- ORCID
- Chen, Ao
- Sun, Yidi
- Lei, Ying
- Li, Chao
- Liao, Sha
- Meng, Juan
- Bai, Yiqin
- Yang, Hao
- Wu, Zihan
- Lin, Feng
- Wang, Kexin
- Li, Mei
- Fei, Tianyi
- Zhuang, Zhenkun
- Huang, Yiming
- Zhang, Yong
- Zhang, Ruiyi
- Han, Lei
- Sun, Xing
- Chen, Bichao
- Li, Wenjiao
- Ma, Kailong
- Wang, He
- Zhang, Huifang
- Wang, Yaqian
- Liu, Xing
- Peng, Jian
- Liu, Chuanyu
- Chen, Wei
- Pan, Wentao
- Xia, Shihui
- Wang, Mingli
- Song, Xinxiang
- Wang, Zhifeng
- Huang, Xin
- Yuan, Yue
- Zhao, Yun
- Chai, Qinwen
- Tan, Xing
- Li, Shengkang
- Huang, Yaling
- Li, Min
- Jin, Mengmeng
- Li, Yan
- Zhang, Hui
- Sun, Suhong
- Gao, Li
- Bai, Yinqi
- Hu, Guohai
- Liu, Shiping
- Wang, Bo
- Li, Huanhuan
- Chen, Mengni
- Wang, Shiwen
- Li, Minglong
- Liu, Weibin
- Liu, Xin
- Zhao, Qian
- Lisby, Michael
- Wang, Jing
- Xie, Qing
- He, Jie
- Xu, Huatai
- Huang, Wei
- Mulder, Jan
- Yang, Huanming
- Wang, Jian
- Yao, Jianhua
- Wei, Wu
- Li, Yuxiang
- Shen, Zhiming
- Liu, Longqi
- Liu, Zhiyong
- Xu, Xun
- Li, Chengyu
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2023-08
- Volume
- 186
- Issue
- 17
- Pages
- 3726-3743.e24
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W4384071384
- Cited by
- 232
- References
- 122
- Citations by year
- 2026: 57 · 2025: 81 · 2024: 65 · 2023: 26
- FWCI
- 20.41
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- Funders
- National Natural Science Foundation of China (2018SHZDZX05, 31827803, 31900466)
- Chinese Academy of Sciences (153D31KYSB20170059, 2018SHZDZX05, XDB32010100)
- Shenzhen Fundamental Research Program
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- macaque cortex, cortical cell types, single-nucleus RNA sequencing, spatial transcriptomics, cell type atlas, cortical layers, cortical regions, glutamatergic neurons, GABAergic neurons, non-neuronal cells, layer 4, cross-species comparison, primate brain evolution
- MeSH terms
- Animals, Cerebral Cortex, Humans, Macaca, Mice, Single-Cell Analysis, Transcriptome
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