Chromatin unwinding state for in situ identification and lineage tracing of circulating tumor cells

Bin Ye; Zhen Wang; Yinqi Bai; Xu Zhang; Rui Zhang; Jingru Lian; Xuefei Liu; Yan Zhang; Zhiyuan Xu; Li Yang; Haiman Jin; Fang Chen; Zhihao Xie; Ping Zhou; Jun Tan; Shan Zeng; Changzheng Du; Yang Min; Xiaomin Ni; Jingxian Duan; Zhicheng Li; Hui Yang; Yunpeng Cai; Hongyan Wu; Catherine C. Liu; Jing Cai; Yi Lu; Jian Zhang; Hao Wu; Hairong Zheng; Longqi Liu; Xin Hong; Hao Yu

doi:10.1002/imt2.70119

iMeta ›› 2026, Vol. 5 ›› Issue (2) :e70119 DOI: 10.1002/imt2.70119

CORRESPONDENCE

Chromatin unwinding state for in situ identification and lineage tracing of circulating tumor cells

Bin Ye ¹^,²^,³
, Zhen Wang ¹
, Yinqi Bai ⁴
, Xu Zhang ⁵
, Rui Zhang ⁶
, Jingru Lian ³
, Xuefei Liu ³
, Yan Zhang ⁷
, Zhiyuan Xu ⁷
, Li Yang ⁷
, Haiman Jin ⁷
, Fang Chen ⁷
, Zhihao Xie ⁸
, Ping Zhou ⁸
, Jun Tan ⁹
, Shan Zeng ¹⁰
, Changzheng Du ³
, Yang Min ¹
, Xiaomin Ni ¹
, Jingxian Duan ¹
, Zhicheng Li ¹
, Hui Yang ¹
, Yunpeng Cai ⁶
, Hongyan Wu ⁶
, Catherine C. Liu ¹¹
, Jing Cai ¹²
, Yi Lu ¹³^,¹⁴
, Jian Zhang ¹³^,¹⁴^,¹⁵
, Hao Wu ¹⁶
, Hairong Zheng ¹^,¹⁷
, Longqi Liu ⁴
, Xin Hong ³^,¹⁸^,¹⁹
, Hao Yu ¹^,¹⁷^,²⁰

Author information +

¹. Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China

². School of Life Sciences and Medical Engineering, Anhui University, Hefei, China

³. Department of Biochemistry, SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, China

⁴. BGI-Research, Hangzhou, China

⁵. School of Mathematical Sciences, South China Normal University, Guangzhou, China

⁶. Research Center for Biomedical Information Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China

⁷. Department of Clinical Oncology, University of Hong Kong-Shenzhen Hospital, Shenzhen, China

⁸. Department of Radiotherapy, The First Affiliated Hospital of Hainan Medical University, Haikou, China

⁹. Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China

¹⁰. Department of Oncology, Xiangya Hospital, Central South University, Changsha, China

¹¹. Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong, China

¹². Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China

¹³. Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, China

¹⁴. Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China

¹⁵. Clinical Research Center, the First People's Hospital of Foshan (The Affiliated Foshan Hospital of Southern University of Science and Technology), School of Medicine, Southern University of Science and Technology, Shenzhen, China

¹⁶. Faculty of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China

¹⁷. The Key Laboratory of Biomedical Imaging Science and System, Chinese Academy of Sciences, Shenzhen, China

¹⁸. Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China

¹⁹. Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China

²⁰. Department of Biomedical Engineering, Shenzhen University of Advanced Technology, Shenzhen, China

hr.zheng@siat.ac.cn

liulongqi@genomics.cn

hongx@sustech.edu.cn

hao.yu@siat.ac.cn

Show less

History +

PDF (2623KB)

Cite this article

Download citation ▾

Bin Ye, Zhen Wang, Yinqi Bai, Xu Zhang, Rui Zhang, Jingru Lian, Xuefei Liu, Yan Zhang, Zhiyuan Xu, Li Yang, Haiman Jin, Fang Chen, Zhihao Xie, Ping Zhou, Jun Tan, Shan Zeng, Changzheng Du, Yang Min, Xiaomin Ni, Jingxian Duan, Zhicheng Li, Hui Yang, Yunpeng Cai, Hongyan Wu, Catherine C. Liu, Jing Cai, Yi Lu, Jian Zhang, Hao Wu, Hairong Zheng, Longqi Liu, Xin Hong, Hao Yu. Chromatin unwinding state for in situ identification and lineage tracing of circulating tumor cells. iMeta, 2026, 5 (2) : e70119 DOI:10.1002/imt2.70119

登录浏览全文

4963

注册一个新账户忘记密码

References

Publishing order | Descend order by publishing year | Descend order by cited within

[1]

Franken, André, Annika Kraemer, Alicia Sicking, Meike Watolla, Mahdi Rivandi, Liwen Yang, Jens Warfsmann, et al. 2023. “Comparative Analysis of EpCAM High-Expressing and Low-Expressing Circulating Tumour Cells With Regard to Their Clonal Relationship and Clinical Value.” British Journal of Cancer 128: 1742–52. https://doi.org/10.1038/s41416-023-02179-0

[2]	Cheng, Yixin, Guanyin Huang, Xuefei Liu, Chun Wu, Jingru Lian, Jing Cao, Lianhui Duan, et al. 2025. “Fusion of Tumor Cells With Lipid-Associated Macrophages Drives Metastatic Progression of Breast Cancer.” Cancer Research 86: 661–78. https://doi.org/10.1158/0008-5472.CAN-25-0261

[3]	Liu, Xiaowei, Jinen Song, Hao Zhang, Xinyu Liu, Fengli Zuo, Yunuo Zhao, Yujie Zhao, et al. 2023. “Immune Checkpoint HLA-E:CD94-NKG2A Mediates Evasion of Circulating Tumor Cells from NK Cell Surveillance.” Cancer Cell 41: 272–87.e9. https://doi.org/10.1016/j.ccell.2023.01.001

[4]

Riethdorf, Sabine, Herbert Fritsche, Volkmar Müller, Thomas Rau, Christian Schindlbeck, Brigitte Rack, Wolfgang Janni, et al. 2007. “Detection of Circulating Tumor Cells in Peripheral Blood of Patients with Metastatic Breast Cancer: A Validation Study of the CellSearch System.” Clinical Cancer Research 13: 920–8. https://doi.org/10.1158/1078-0432.CCR-06-1695

[5]

Burr, Risa, Jon F. Edd, Brian Chirn, Avanish Mishra, Daniel A. Haber, Mehmet Toner, and Shyamala Maheswaran. 2022. “Negative-Selection Enrichment of Circulating Tumor Cells From Peripheral Blood Using the Microfluidic CTC-iChip.” In Mammary Stem Cells: Methods and Protocols, 309–21. New York, NY: Humana. https://doi.org/10.1007/978-1-0716-2193-6_18

[6]	Nofech-Mozes, Ido, David Soave, Philip Awadalla, and Sagi Abelson. 2023. “Pan-Cancer Classification of Single Cells in the Tumour Microenvironment.” Nature Communications 14: 1615. https://doi.org/10.1038/s41467-023-37353-8

[7]	Gao, Ruli, Shanshan Bai, Ying C. Henderson, Yiyun Lin, Aislyn Schalck, Yun Yan, Tapsi Kumar, et al. 2021. “Delineating Copy Number and Clonal Substructure in Human Tumors From Single-Cell Transcriptomes.” Nature Biotechnology 39: 599–608. https://doi.org/10.1038/s41587-020-00795-2

[8]	Cui, Haotian, Chloe Wang, Hassaan Maan, Kuan Pang, Fengning Luo, Nan Duan, and Bo Wang. 2024. “scGPT: Toward Building a Foundation Model for Single-Cell Multi-Omics Using Generative AI.” Nature Methods 21: 1470–80. https://doi.org/10.1038/s41592-024-02201-0

[9]	Hao, Minsheng, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, et al. 2024. “Large-Scale Foundation Model on Single-Cell Transcriptomics.” Nature Methods 21: 1481–91. https://doi.org/10.1038/s41592-024-02305-7

[10]	Guo, Xiaoxu, Fanghe Lin, Chuanyou Yi, Juan Song, Di Sun, Li Lin, Zhixing Zhong, et al. 2022. “Deep Transfer Learning Enables Lesion Tracing of Circulating Tumor Cells.” Nature Communications 13: 7687. https://doi.org/10.1038/s41467-022-35296-0

[11]	Iyer, Arvind, Krishan Gupta, Shreya Sharma, Kishore Hari, Yi Lee, Neevan Ramalingam, Yoon Yap, et al. 2020. “Integrative Analysis and Machine Learning Based Characterization of Single Circulating Tumor Cells.” Journal of Clinical Medicine 9: 1206. https://doi.org/10.3390/jcm9041206

[12]

Bancaud, Aurélien, Sébastien Huet, Nathalie Daigle, Julien Mozziconacci, Joël Beaudouin, and Jan Ellenberg. 2009. “Molecular Crowding Affects Diffusion and Binding of Nuclear Proteins in Heterochromatin and Reveals the Fractal Organization of Chromatin.” The EMBO Journal 28: 3785–98. https://doi.org/10.1038/emboj.2009.340

[13]	Gibcus, Johan H., and Job Dekker. 2013. “The Hierarchy of the 3D Genome.” Molecular Cell 49: 773–82. https://doi.org/10.1016/j.molcel.2013.02.011

[14]

Taftaf, Rokana, Xia Liu, Salendra Singh, Yuzhi Jia, Nurmaa K. Dashzeveg, Andrew D. Hoffmann, Lamiaa El-Shennawy, et al. 2021. “ICAM1 Initiates CTC Cluster Formation and Trans-Endothelial Migration in Lung Metastasis of Breast Cancer.” Nature Communications 12: 4867. https://doi.org/10.1038/s41467-021-25189-z

[15]	Pereira-Veiga, Thais, Svenja Schneegans, Klaus Pantel, and Harriet Wikman. 2022. “Circulating Tumor Cell-Blood Cell Crosstalk: Biology and Clinical Relevance.” Cell Reports 40: 111298. https://doi.org/10.1016/j.celrep.2022.111298

[16]

Rosen, David B., Jayaram Bettadapura, Mohammed Alsharifi, Porunelloor A. Mathew, Hilary S. Warren, and Lewis L. Lanier. 2005. “Cutting Edge: Lectin-Like Transcript-1 Is a Ligand for the Inhibitory Human NKR-P1A Receptor.” The Journal of Immunology 175: 7796–9. https://doi.org/10.4049/jimmunol.175.12.7796

[17]

Germain, Claire, Franck Bihl, Stefan Zahn, Gwenola Poupon, Marie-Jeanne Dumaurier, Hariniaina Henintsoa Rampanarivo, Søren Berg Padkjær, Pieter Spee, and Veronique M. Braud. 2010. “Characterization of Alternatively Spliced Transcript Variants of CLEC2D Gene.” Journal of Biological Chemistry 285: 36207–15. https://doi.org/10.1074/jbc.M110.179622

[18]

Osmani, Naël, Gautier Follain, María J. García León, Olivier Lefebvre, Ignacio Busnelli, Annabel Larnicol, Sébastien Harlepp, and Jacky G. Goetz. 2019. “Metastatic Tumor Cells Exploit Their Adhesion Repertoire to Counteract Shear Forces During Intravascular Arrest.” Cell Reports 28: 2491–500.e5. https://doi.org/10.1016/j.celrep.2019.07.102

[19]	Zheng, Xiaocui, Xinjing Wang, Xi Cheng, Zhaoyuan Liu, Yujia Yin, Xiaoduan Li, Zhihao Huang, et al. 2023. “Single-Cell Analyses Implicate Ascites in Remodeling the Ecosystems of Primary and Metastatic Tumors in Ovarian Cancer.” Nature Cancer 4: 1138–56. https://doi.org/10.1038/s43018-023-00599-8

[20]	Cohen, Stacey A., Minetta C. Liu, and Alexey Aleshin. 2023. “Practical Recommendations for Using ctDNA in Clinical Decision Making.” Nature 619: 259–68. https://doi.org/10.1038/s41586-023-06225-y