ArticleNature genetics2024
A spatiotemporal atlas of mouse liver homeostasis and regeneration.
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Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53citing papers in PubMed
13.8field-weighted citation impact, top 1% of its field
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53 citing papers in PubMed, 59 citations in OpenAlex.
- Solute Carrier Family 1 Member 5 (SLC1A5)-dependent glutamine transport regulates macrophage senescence and efferocytosis during liver regeneration.Molecular biomedicine · 2026Article
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- Haemodynamic control of zonated liver function via instructive vascular Wnt signalling.Nature communications · 2026Article
- Adaptive oncogenesis of β-catenin emerges from declining liver tissue integrity.Nature communications · 2026Article
- Succinic acid inhibits hepatocyte regenerative signaling via STAT3 SH2-domain engagement.Molecular biomedicine · 2026Article
- Hepatic Mechanisms and Therapeutic Target Underpinning Hypercoagulation in Obesity: Insights From Genetic and Transcriptomic Analyses.Exploration (Beijing, China) · 2026Article
- Next-Generation Hepatocyte Expansion: Bridging Molecular Reprogramming with Multicellular Organoids for Clinical Translation.Stem cell reviews and reports · 2026Review
- Single-Cell Annotation and Localization via Integrating Spatial Transcriptomics Maps the Mouse Ocular Atlas and RAO Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Segmental specification of the human female fetal reproductive tract revealed by spatiotemporal dynamics.Nature cell biology · 2026Article
- EasySCP unveils extensive liver zonation at single-cell proteomics resolution.Nature communications · 2026Article
- SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics.NAR genomics and bioinformatics · 2026Article
- Glutathione peroxidase 3 preserves hepatocyte mitochondrial quality control to enhance macrophage pro-regenerative phenotype during liver regeneration.Clinical and translational medicine · 2026Article
- Spatiotemporal Transcriptomics Characterizes Immune Microenvironment During Mouse Liver Aging.Aging cell · 2026Article
- [Research advances on hepatocyte zonal changes in metabolic associated fatty liver disease].Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology · 2026Review
- Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics.Nature communications · 2026Article
- Signal control during tissue regeneration in adult animals.Nature reviews. Molecular cell biology · 2026Review
- Scalable discovery of spatial multicellular patterns via neighborhood-to-sequence transformation.Communications biology · 2026Article
- Single-cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue architecture.Nature metabolism · 2026Article
- Conversion of Transplanted Mature Hepatocytes into AfpAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- stGrads: decoding spatial gene expression gradients through proximity-driven analysis in complex tissues.Briefings in bioinformatics · 2026Article
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Authors and funding
58 authors at 14 institutions in 8 countries.
Jiangshan Xu *BGI Research, Hangzhou, China.
Pengcheng Guo *State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China. guopengcheng@genomics.cn.
Shijie Hao *BGI Research, Hangzhou, China.ORCID http://orcid.org/0000-0001-9845-3101
Shuncheng Shangguan *BGI Research, Shenzhen, China.
Quan Shi *Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Giacomo Volpe *Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy.ORCID http://orcid.org/0000-0001-5000-6951
Keke HuangFaculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
Jing ZuoBGI Research, Hangzhou, China.
Juan AnSchool of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
Yue YuanBGI Research, Hangzhou, China.
Mengnan ChengBGI Research, Hangzhou, China.
Qiuting DengBGI Research, Hangzhou, China.
Xiao ZhangState Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
Guangyao LaiJoint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China.
Haitao NanState Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
Baihua WuState Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
Xinyi ShentuState Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
Liang WuLaboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
Xiaoyu WeiBGI Research, Hangzhou, China.
Yujia JiangBGI Research, Hangzhou, China.
Xin HuangBGI Research, Shenzhen, China.
Fengyu PanBGI Research, Hangzhou, China.
Yumo SongBGI Research, Hangzhou, China.
Ronghai LiBGI Research, Hangzhou, China.
Zhifeng WangBGI Research, Hangzhou, China.
Chuanyu LiuBGI Research, Hangzhou, China.ORCID http://orcid.org/0000-0003-2258-0897
Shiping LiuBGI Research, Hangzhou, China.ORCID http://orcid.org/0000-0003-0019-619X
Yuxiang LiBGI Research, Shenzhen, China.
Tao YangChina National GeneBank, BGI Research, Shenzhen, China.ORCID http://orcid.org/0000-0003-4211-5183
Zhicheng XuChina National GeneBank, BGI Research, Shenzhen, China.
Wensi DuChina National GeneBank, BGI Research, Shenzhen, China.
Ling LiChina National GeneBank, BGI Research, Shenzhen, China.
Tanveer AhmedGuangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
Kai YouGuangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
Zhen DaiGuangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
Li LiLaboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
Baoming QinGuangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.ORCID http://orcid.org/0000-0001-7652-161X
Yinxiong LiGuangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.ORCID http://orcid.org/0000-0001-8331-9903
Liangxue LaiGuangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.ORCID http://orcid.org/0000-0002-5256-6802
Dajiang QinThe Fifth Affiliated Hospital of Guangzhou Medical University-BGI Research Center for Integrative Biology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
Junling ChenDepartment of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China.
Rong FanDepartment of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China.
Yongyin LiDepartment of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China.
Jinlin HouDepartment of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China.ORCID http://orcid.org/0000-0001-8230-8583
Michael OttDepartment of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.
Amar Deep SharmaDepartment of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.
Tobias CantzDepartment of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.
Axel SchambachDivision of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-2743-0070
Karsten KristiansenDepartment of Biology, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-6024-0917
Andrew P HutchinsShenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.ORCID http://orcid.org/0000-0001-7784-2255
Berthold GöttgensDepartment of Haematology and Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0001-6302-5705
Patrick H MaxwellCambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-0338-2679
Lijian HuiState Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.ORCID http://orcid.org/0000-0002-6213-6187
Xun XuBGI Research, Hangzhou, China. xuxun@genomics.cn.ORCID http://orcid.org/0000-0002-5338-5173
Longqi LiuBGI Research, Hangzhou, China. liulongqi@genomics.cn.ORCID http://orcid.org/0000-0002-5828-5542
Ao ChenBGI Research, Shenzhen, China. chenao@genomics.cn.ORCID http://orcid.org/0000-0002-9699-8340
Yiwei LaiBGI Research, Hangzhou, China. laiyiwei@genomics.cn.ORCID http://orcid.org/0000-0003-0733-812X
Miguel A EstebanState Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China. miguelesteban@genomics.cn.ORCID http://orcid.org/0000-0002-1426-6809
BGI Group (China) · CNChinese Academy of Sciences · CNMedizinische Hochschule Hannover · DENanfang Hospital · CNUniversity of Copenhagen · DKBoston Children's Hospital · USChulalongkorn University · THIstituto Tumori Bari · ITJilin University · CNSouthern University of Science and Technology · CNUniversity of Cambridge · GBUniversity of Science and Technology of China · CNWellcome/MRC Cambridge Stem Cell Institute · GBXinjiang Medical University · CN
Funding
Medical Research Council MC_PC_17230National Natural Science Foundation of China (National Science Foundation of China) 32200688National Natural Science Foundation of China (National Science Foundation of China) 32370848National Natural Science Foundation of China (National Science Foundation of China) 92168202
Abstract
The mechanism by which mammalian liver cell responses are coordinated during tissue homeostasis and perturbation is poorly understood, representing a major obstacle in our understanding of many diseases. This knowledge gap is caused by the difficulty involved with studying multiple cell types in different states and locations, particularly when these are transient. We have combined Stereo-seq (spatiotemporal enhanced resolution omics-sequencing) with single-cell transcriptomic profiling of 473,290 cells to generate a high-definition spatiotemporal atlas of mouse liver homeostasis and regeneration at the whole-lobe scale. Our integrative study dissects in detail the molecular gradients controlling liver cell function, systematically defining how gene networks are dynamically modulated through intercellular communication to promote regeneration. Among other important regulators, we identified the transcriptional cofactor TBL1XR1 as a rheostat linking inflammation to Wnt/β-catenin signaling for facilitating hepatocyte proliferation. Our data and analytical pipelines lay the foundation for future high-definition tissue-scale atlases of organ physiology and malfunction.
Indexed as
HomeostasisLiverLiver RegenerationWnt Signaling PathwayAnimalsCell ProliferationGene Expression ProfilingGene Regulatory NetworksHepatocytesMaleMiceMice, Inbred C57BLReceptors, Cytoplasmic and NuclearSingle-Cell AnalysisTranscriptomeReceptors, Cytoplasmic and Nuclear
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