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Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex

Author

Listed:
  • Ying Lei

    (BGI-Hangzhou
    BGI-Shenzhen
    Shenzhen Bay Laboratory)

  • Mengnan Cheng

    (BGI-Hangzhou
    BGI-Shenzhen)

  • Zihao Li

    (BGI-Hangzhou
    University of Chinese Academy of Sciences)

  • Zhenkun Zhuang

    (BGI-Hangzhou
    South China University of Technology)

  • Liang Wu

    (BGI-Shenzhen)

  • Yunong sun

    (BGI-Hangzhou
    University of Chinese Academy of Sciences)

  • Lei Han

    (BGI-Hangzhou
    BGI-Shenzhen
    Shenzhen Bay Laboratory)

  • Zhihao Huang

    (BGI-Shenzhen)

  • Yuzhou Wang

    (BGI-Shenzhen)

  • Zifei Wang

    (BGI-Shenzhen)

  • Liqin Xu

    (BGI-Shenzhen)

  • Yue Yuan

    (BGI-Hangzhou)

  • Shang Liu

    (BGI-Shenzhen)

  • Taotao Pan

    (BGI-Shenzhen)

  • Jiarui Xie

    (BGI-Shenzhen)

  • Chuanyu Liu

    (BGI-Hangzhou)

  • Giacomo Volpe

    (IRCCS-Istituto Tumori “Giovanni Paolo II”. Viale O Flacco 65)

  • Carl Ward

    (Guangzhou Institutes of Biomedicine and Health, CAS)

  • Yiwei Lai

    (BGI-Hangzhou
    Guangzhou Institutes of Biomedicine and Health, CAS)

  • Jiangshan Xu

    (BGI-Hangzhou)

  • Mingyue Wang

    (BGI-Hangzhou)

  • Hao Yu

    (BGI-Shenzhen)

  • Haixi Sun

    (BGI-Shenzhen)

  • Qichao Yu

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Liang Wu

    (BGI-Shenzhen)

  • Chunqing Wang

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Chi Wai Wong

    (Huazhen Biosciences)

  • Wei Liu

    (Huazhen Biosciences)

  • Liangzhi Xu

    (Huazhen Biosciences)

  • Jingkuan Wei

    (Kunming University of Science and Technology)

  • Dandan Chen

    (BGI-GenoImmune, BGI-Shenzhen)

  • Zhouchun Shang

    (BGI-Shenzhen
    MGI, BGI-Shenzhen)

  • Guibo Li

    (BGI-Shenzhen)

  • Kun Ma

    (BGI-Shenzhen)

  • Le Cheng

    (BGI-Yunnan, BGI-Shenzhen)

  • Fei Ling

    (South China University of Technology)

  • Tao Tan

    (Kunming University of Science and Technology)

  • Kai Chen

    (Kunming University of Science and Technology)

  • Bosiljka Tasic

    (Allen Institute for Brain Science)

  • Michael Dean

    (Cancer and Inflammation Program, National Cancer Institute at Frederick, Building 560)

  • Weizhi Ji

    (Kunming University of Science and Technology)

  • Huanming Yang

    (BGI-Shenzhen
    James D. Watson Institute of Genome Sciences)

  • Ying Gu

    (BGI-Hangzhou
    BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Miguel A. Esteban

    (BGI-Hangzhou
    Guangzhou Institutes of Biomedicine and Health, CAS
    Chinese Academy of Sciences)

  • Yuxiang Li

    (BGI-Shenzhen)

  • Ao Chen

    (BGI-Shenzhen)

  • Yuyu Niu

    (Kunming University of Science and Technology
    Kunming University of Science and Technology)

  • Hongkui Zeng

    (Allen Institute for Brain Science)

  • Yong Hou

    (BGI-Shenzhen
    Shenzhen Bay Laboratory
    Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen)

  • Longqi Liu

    (BGI-Hangzhou
    BGI-Shenzhen
    Shenzhen Bay Laboratory
    Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen)

  • Shiping Liu

    (BGI-Hangzhou
    BGI-Shenzhen
    Shenzhen Bay Laboratory
    Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen)

  • Xun Xu

    (BGI-Hangzhou
    BGI-Shenzhen
    Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen)

Abstract

Single cell approaches have increased our knowledge about the cell type composition of the non-human primate (NHP), but a detailed characterization of area-specific regulatory features remains outstanding. We generated single-cell transcriptomic and chromatin accessibility (single-cell ATAC) data of 358,237 cells from prefrontal cortex (PFC), primary motor cortex (M1) and primary visual cortex (V1) of adult female cynomolgus monkey brain, and integrated this dataset with Stereo-seq (spatial enhanced resolution omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular states. We identified area-specific chromatin accessible sites and their targeted genes, including the cell type-specific transcriptional regulatory network associated with excitatory neurons heterogeneity. We reveal calcium ion transport and axon guidance genes related to specialized functions of PFC and M1, identified the similarities and differences between adult macaque and human oligodendrocyte trajectories, and mapped the genetic variants and gene perturbations of human diseases to NHP cortical cells. This resource establishes a transcriptomic and chromatin accessibility combinatory regulatory landscape at a single-cell and spatially resolved resolution in NHP cortex.

Suggested Citation

  • Ying Lei & Mengnan Cheng & Zihao Li & Zhenkun Zhuang & Liang Wu & Yunong sun & Lei Han & Zhihao Huang & Yuzhou Wang & Zifei Wang & Liqin Xu & Yue Yuan & Shang Liu & Taotao Pan & Jiarui Xie & Chuanyu L, 2022. "Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34413-3
    DOI: 10.1038/s41467-022-34413-3
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    References listed on IDEAS

    as
    1. Ryan S. Ziffra & Chang N. Kim & Jayden M. Ross & Amy Wilfert & Tychele N. Turner & Maximilian Haeussler & Alex M. Casella & Pawel F. Przytycki & Kathleen C. Keough & David Shin & Derek Bogdanoff & Ana, 2021. "Single-cell epigenomics reveals mechanisms of human cortical development," Nature, Nature, vol. 598(7879), pages 205-213, October.
    2. Rebecca D. Hodge & Trygve E. Bakken & Jeremy A. Miller & Kimberly A. Smith & Eliza R. Barkan & Lucas T. Graybuck & Jennie L. Close & Brian Long & Nelson Johansen & Osnat Penn & Zizhen Yao & Jeroen Egg, 2019. "Conserved cell types with divergent features in human versus mouse cortex," Nature, Nature, vol. 573(7772), pages 61-68, September.
    3. Trygve E. Bakken & Nikolas L. Jorstad & Qiwen Hu & Blue B. Lake & Wei Tian & Brian E. Kalmbach & Megan Crow & Rebecca D. Hodge & Fenna M. Krienen & Staci A. Sorensen & Jeroen Eggermont & Zizhen Yao & , 2021. "Comparative cellular analysis of motor cortex in human, marmoset and mouse," Nature, Nature, vol. 598(7879), pages 111-119, October.
    4. Sarah Jäkel & Eneritz Agirre & Ana Mendanha Falcão & David Bruggen & Ka Wai Lee & Irene Knuesel & Dheeraj Malhotra & Charles ffrench-Constant & Anna Williams & Gonçalo Castelo-Branco, 2019. "Altered human oligodendrocyte heterogeneity in multiple sclerosis," Nature, Nature, vol. 566(7745), pages 543-547, February.
    5. Bosiljka Tasic & Zizhen Yao & Lucas T. Graybuck & Kimberly A. Smith & Thuc Nghi Nguyen & Darren Bertagnolli & Jeff Goldy & Emma Garren & Michael N. Economo & Sarada Viswanathan & Osnat Penn & Trygve B, 2018. "Shared and distinct transcriptomic cell types across neocortical areas," Nature, Nature, vol. 563(7729), pages 72-78, November.
    6. Hansruedi Mathys & Jose Davila-Velderrain & Zhuyu Peng & Fan Gao & Shahin Mohammadi & Jennie Z. Young & Madhvi Menon & Liang He & Fatema Abdurrob & Xueqiao Jiang & Anthony J. Martorell & Richard M. Ra, 2019. "Author Correction: Single-cell transcriptomic analysis of Alzheimer’s disease," Nature, Nature, vol. 571(7763), pages 1-1, July.
    7. Senlin Yin & Keying Lu & Tao Tan & Jie Tang & Jingkuan Wei & Xu Liu & Xinlei Hu & Haisu Wan & Wei Huang & Yong Fan & Dan Xie & Yang Yu, 2020. "Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    8. Trygve E. Bakken & Jeremy A. Miller & Song-Lin Ding & Susan M. Sunkin & Kimberly A. Smith & Lydia Ng & Aaron Szafer & Rachel A. Dalley & Joshua J. Royall & Tracy Lemon & Sheila Shapouri & Kaylynn Aion, 2016. "A comprehensive transcriptional map of primate brain development," Nature, Nature, vol. 535(7612), pages 367-375, July.
    9. Hansruedi Mathys & Jose Davila-Velderrain & Zhuyu Peng & Fan Gao & Shahin Mohammadi & Jennie Z. Young & Madhvi Menon & Liang He & Fatema Abdurrob & Xueqiao Jiang & Anthony J. Martorell & Richard M. Ra, 2019. "Single-cell transcriptomic analysis of Alzheimer’s disease," Nature, Nature, vol. 570(7761), pages 332-337, June.
    10. Zizhen Yao & Hanqing Liu & Fangming Xie & Stephan Fischer & Ricky S. Adkins & Andrew I. Aldridge & Seth A. Ament & Anna Bartlett & M. Margarita Behrens & Koen Berge & Darren Bertagnolli & Hector Roux , 2021. "A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex," Nature, Nature, vol. 598(7879), pages 103-110, October.
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    1. Tingting Bo & Jie Li & Ganlu Hu & Ge Zhang & Wei Wang & Qian Lv & Shaoling Zhao & Junjie Ma & Meng Qin & Xiaohui Yao & Meiyun Wang & Guang-Zhong Wang & Zheng Wang, 2023. "Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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