Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution

Rong Xiang¹, Junmin Wang², Zhan Chen¹, Jin Tao², Qinfeng Peng², Ruoqi Ding², Tao Zhou¹, Zhencheng Tu¹, Shaoshuai Wang², Tao Yang³, Jing Chen³, Zihan Jia¹, Xueping Li², Xinru Zhang², Shuai Chen⁴, Nannan Cheng², Mengke Zhao², Jiaxin Li², Qidi Xue², Houlian Zhang², Chao Jiang⁴, Na Xing⁵, Kang Ouyang¹, Albert Pekny⁶, Malgorzata M Michalowska⁶, Yolanda de Pablo⁶, Ulrika Wilhelmsson⁶, Nicholas Mitsios⁷, Chuanyu Liu⁸, Xun Xu⁹, Xiaochong Fan¹⁰, Marcela Pekna¹¹, Milos Pekny¹², Xuemei Chen¹³, Longqi Liu¹⁴, Jan Mulder¹⁵, Mingyue Wang¹⁶, Jian Wang¹⁷

Affiliations

¹ BGI Research, Hangzhou 310030, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
² Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
³ China National GeneBank, BGI Research, Shenzhen 518120, China.
⁴ Department of Neurology, The People's Hospital of Zhengzhou University & Henan Provincial People's Hospital, Zhengzhou 450003, China.
⁵ Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
⁶ Laboratory of Astrocyte Biology and CNS Regeneration, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg 405 30 Sweden.
⁷ Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden.
⁸ BGI Research, Hangzhou 310030, China; BGI Research, Shenzhen 518083, China; Shanxi Medical University, BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China.
⁹ BGI Research, Hangzhou 310030, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China; Shanxi Medical University, BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China.
¹⁰ Department of Pain Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
¹¹ Laboratory of Regenerative Neuroimmunology, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg 40530, Sweden.
¹² Laboratory of Astrocyte Biology and CNS Regeneration, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg 405 30 Sweden; University of Newcastle, Newcastle, NSW 2308, Australia; Florey Institute of Neuroscience and Mental Health, Parkville VIC 3052, Australia. Electronic address: milos.pekny@neuro.gu.se.
¹³ Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China. Electronic address: chenxm@zzu.edu.cn.
¹⁴ BGI Research, Hangzhou 310030, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China; Shanxi Medical University, BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China. Electronic address: liulongqi@genomics.cn.
¹⁵ Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden. Electronic address: jan.mulder@ki.se.
¹⁶ BGI Research, Hangzhou 310030, China; Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China. Electronic address: wangmingyue@genomics.cn.
¹⁷ Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China. Electronic address: jianwang2020@outlook.com.

PMID: 40412375
DOI: 10.1016/j.neuron.2025.04.026

Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution

Rong Xiang et al. Neuron. 2025.

. 2025 Jul 9;113(13):2102-2122.e7.

doi: 10.1016/j.neuron.2025.04.026. Epub 2025 May 24.

Authors

Affiliations

¹ BGI Research, Hangzhou 310030, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
² Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
³ China National GeneBank, BGI Research, Shenzhen 518120, China.
⁴ Department of Neurology, The People's Hospital of Zhengzhou University & Henan Provincial People's Hospital, Zhengzhou 450003, China.
⁵ Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
⁶ Laboratory of Astrocyte Biology and CNS Regeneration, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg 405 30 Sweden.
⁷ Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden.
⁸ BGI Research, Hangzhou 310030, China; BGI Research, Shenzhen 518083, China; Shanxi Medical University, BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China.
⁹ BGI Research, Hangzhou 310030, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China; Shanxi Medical University, BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China.
¹⁰ Department of Pain Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
¹¹ Laboratory of Regenerative Neuroimmunology, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg 40530, Sweden.
¹² Laboratory of Astrocyte Biology and CNS Regeneration, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg 405 30 Sweden; University of Newcastle, Newcastle, NSW 2308, Australia; Florey Institute of Neuroscience and Mental Health, Parkville VIC 3052, Australia. Electronic address: milos.pekny@neuro.gu.se.
¹³ Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China. Electronic address: chenxm@zzu.edu.cn.
¹⁴ BGI Research, Hangzhou 310030, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China; Shanxi Medical University, BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China. Electronic address: liulongqi@genomics.cn.
¹⁵ Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden. Electronic address: jan.mulder@ki.se.
¹⁶ BGI Research, Hangzhou 310030, China; Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518005, China. Electronic address: wangmingyue@genomics.cn.
¹⁷ Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China. Electronic address: jianwang2020@outlook.com.

PMID: 40412375
DOI: 10.1016/j.neuron.2025.04.026

Abstract

Intracerebral hemorrhage (ICH) is a prevalent disease with high mortality. Despite advances in clinical care, the prognosis of ICH remains poor due to an incomplete understanding of the complex pathological processes. To address this challenge, we generated single-cell-resolution spatiotemporal transcriptomic maps of the mouse brain following ICH. This dataset is the most extensive resource available, providing detailed information about the temporal expression of genes along with a high-resolution cellular profile and preserved cellular organization. We identified 100 distinct cell subclasses, 17 of which were found to play significant roles in the pathophysiology of ICH. We also report similarities and differences between two experimental ICH models and human postmortem ICH brain tissue. This study advances the understanding of the local and global responses of brain cells to ICH. It provides a valuable resource that can facilitate future research and aid the development of novel therapies for this devastating condition.

Keywords: brain repair; glial scar; intracerebral hemorrhage; neuroinflammation; spatial transcriptome.

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Conflict of interest statement

Declaration of interests X.X. and L.L. have stock holdings in BGI.

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Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution

Affiliations

Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution

Authors

Affiliations

Abstract

Conflict of interest statement

MeSH terms

LinkOut - more resources

Full Text Sources