Single-cell multi-omics deciphers hepatocyte dedifferentiation and illuminates maintenance strategies

Jie Hao; Zhenyi Wang; Jilong Ren; Shenghao Cao; Zhongchen Xie; Jinghuan Yang; Jiachen Li; Weizhe Ding; Jie Li; Zhiqiang Han; Ye Yuan; Tang Hai; Sheng Ding; Michael Q. Zhang; Minglei Shi

doi:10.1111/cpr.13772

Cell Proliferation ›› 2025, Vol. 58 ›› Issue (3) : e13772 DOI: 10.1111/cpr.13772

ORIGINAL ARTICLE

Single-cell multi-omics deciphers hepatocyte dedifferentiation and illuminates maintenance strategies

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¹. School of Pharmaceutical Sciences, Tsinghua University, Beijing, China

². MOE Key Laboratory of Bioinformatics, Beijing National Research Center for Information Science and Technology, Bioinformatics Division, Tsinghua University, Beijing, China

³. Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China

⁴. Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China

⁵. Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, Beijing, China

⁶. Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China

⁷. Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China

⁸. School of Life Sciences, Tsinghua University, Beijing, China

⁹. State Key Laboratory of Biopharmaceutical Preparation and Delivery, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China

¹⁰. Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson, Texas, USA

yyuan@ipe.ac.cn

haitang@ioz.ac.cn

shengding@tsinghua.edu.cn

michael.zhang@utdallas.edu

shiml79@hsc.pku.edu.cn

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Abstract

Due to the similarity to human hepatocytes, porcine hepatocytes play an important role in hepatic research and drug evaluation. However, once hepatocytes were cultured in vitro, it was often prone to dedifferentiate, resulting in the loss of their characteristic features and normal functions, which impede their application in liver transplantation and hepatotoxic drugs evaluation. Up to now, this process has yet to be thoroughly investigated from the single-cell resolution and multi-omics perspective. In this study, we utilized 10× multiome technology to dissect the heterogeneity of porcine hepatocytes at different time points (Days 0, 1, 3, 5 and 7) during dedifferentiation. We comprehensively investigated cell heterogeneity, cellular dynamics, signalling pathways, potential gene targets, enhancer-driven gene regulatory networks, cell–cell communications of these cells and the conservation of mechanisms across species. We found that a series of critical signalling pathways driven by ERK, PI3K, Src and TGF-β were activated during this process, especially in the early stage of dedifferentiation. Based on these discoveries, we constructed a chemical combination targeting these pathways, which effectively inhibited the dedifferentiation of porcine hepatocytes in vitro. To validate the effectiveness of this combination, we transplanted such treated hepatocytes into FRGN mice, and the results demonstrated that these cells could effectively repopulate the liver and improve the survival of mice.

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Jie Hao, Zhenyi Wang, Jilong Ren, Shenghao Cao, Zhongchen Xie, Jinghuan Yang, Jiachen Li, Weizhe Ding, Jie Li, Zhiqiang Han, Ye Yuan, Tang Hai, Sheng Ding, Michael Q. Zhang, Minglei Shi. Single-cell multi-omics deciphers hepatocyte dedifferentiation and illuminates maintenance strategies. Cell Proliferation, 2025, 58(3): e13772 DOI:10.1111/cpr.13772

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