Global Spatial Transcriptome of Macaque Brain at Single-Cell Resolution

作者：Ao Chen, Yidi Sun, Ying Lei, Chao Li, Chao Li, Sha Liao, Zhifeng Liang, Feng Lin, Nini Yuan, Mei Li, Kexin Wang, Meisong Yang, Shuzhen Zhang, Zhenkun Zhuang, Juan Meng, Qiong Song, Yong Zhang, Yuanfang Xu, Luman Cui, Lei Han, Hao Yang, Xing Sun, Tianyi Fei, Bichao Chen, Wenjiao Li, Baoqian Huangfu, Kailong Ma, Li Zhao, Yikun Lin, Zhen Liu, Zhen Liu, He Wang, Yanqing Zhong, Huifang Zhang, Qian Yu, Yaqian Wang, Zhiyong Zhu, Xing Liu, Jian Peng, Chuanyu Liu, Wei Chen, Yingjie An, Shihui Xia, Yanbing Lu, Mingli Wang, Xinxiang Song, Shuai Liu, Zhifeng Wang, Chun Gong, Xin Huang, Yue Yuan, Yun Zhao, Zhenhui Luo, Xing Haw Marvin Tan, Jianfeng Liu, Mingyuan Zheng, Shengkang Li, Yaling Huang, Hong Yan, Zirui Huang, Min Li, Ruiyi Zhang, Mengmeng Jin, Yan Li, Yan Li, Hui Zhang, Suhong Sun, Yinqi Bai, Mengnan Cheng, Guohai Hu, Shiping Liu, Bo Wang, Bin Xiang, Shuting Li, Huanhuan Li, Mengni Chen, Shiwen Wang, Qi Zhang, Weibin Liu, Xin Liu, Qian Zhao, Michael Lisby, Jing Wang, Jiao Fang, Zhiyue Lu, Yun Lin, Qing Xie, Jie He, Huatai Xu, Wei Huang, Wu Wei, Huanming Yang, Yan-Gang Sun, Mu‐ming Poo, Jian Wang, Yuxiang Li, Yuxiang Li, Zhiming Shen, Longqi Liu, Zhiyong Liu, Zhiyong Liu, Xun Xu, Chengyu Li, Chengyu Li · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2022 · DOI：10.1101/2022.03.23.485448 · 被引用次数：20 · 研究领域：Single-cell and spatial transcriptomics、Neuroinflammation and Neurodegeneration Mechanisms、Immune cells in cancer

Abstract Global profile of gene expression at single-cell resolution remains to be determined for primates. Using a recently developed technology (“Stereo-seq”), we have obtained a comprehensive single-cell spatial transcriptome map at the whole-brain level for cynomolgus monkeys, with ∼600 genes per cell for 10 μm-thick coronal sections (up to 15 cm 2 in size). Large-scale single-nucleus RNA-seq analysis for ∼1 million cells helped to identify cell types corresponding to Stereo-seq gene expression profiles, providing a 3-D cell type atlas of the monkey brain. Quantitative analysis of Stereo-seq data revealed molecular fingerprints that mark distinct neocortical layers and subregions, as well as domains within subcortical structures including hippocampus, thalamus, striatum, cerebellum, hypothalamus and claustrum. Striking whole-brain topography and coordinated patterns were found in the expression of genes encoding receptors and transporters for neurotransmitters and neuromodulators. These results pave the way for cellular and molecular understanding of organizing principles of the primate brain.