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Single-cell multiomics reveals a gene regulatory circuit driving leukemia cell differentiation

Oncogene volumeĀ 44,Ā pages 1350ā€“1360 (2025) Cite this article

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Abstract

Cancer differentiation therapy aims to induce the maturation of neoplastic cells, but the mechanisms regulating cell fate decisions in oncogenic contexts remain unclear. In this study, we integrated single-cell chromatin accessibility and single-cell transcriptome analyses to explore the regulatory trajectories of a classical PML/RARĪ±+ acute promyeloid leukemia (APL) cell line (NB4) post treatment by all-trans-retinoid acid (ATRA). Our findings indicated that ATRA activated specific PML/RARĪ±-target enhancers to trigger a regulatory circuit composed of a positive feedforward gene regulatory circuit involving two transcription factors, SPI1 and CEBPE. This regulatory circuit was both necessary and sufficient to drive NB4 cells through an intermediate cell fate decision point to initiate terminal granulopoiesis. Moreover, ectopic expression of SPI1 and CEBPE promoted granulocytic differentiation in non-APL leukemia cell lines HL60 and K562. Our study sheds mechanistic insights into the differentiation trajectories induced by ATRA and illustrates a gene regulatory circuit that could be widely applied to promote differentiation of leukemia cells.

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Fig. 1: Heterogeneity in ATRA-induced differentiation of NB4 cells.
The alternative text for this image may have been generated using AI.
Fig. 2: Identification of candidate transcription factors driving ATRA-induced granulocytic differentiation.
The alternative text for this image may have been generated using AI.
Fig. 3: SPI1 and CEBPE drive ATRA-induced granulocytic differentiation.
The alternative text for this image may have been generated using AI.
Fig. 4: Co-accessibility of PML/RARĪ±-binding sites with SPI1 and CEBPE promoters mediate ATRA-induced granulocytic differentiation.
The alternative text for this image may have been generated using AI.
Fig. 5: Cross-regulation of SPI1 and CEBPE establishes a gene regulatory circuit for cell fate transition in NB4 cells.
The alternative text for this image may have been generated using AI.
Fig. 6: Activating SPI1 and CEBPE regulatory circuit enhances myelocytic differentiation in leukemia cells.
The alternative text for this image may have been generated using AI.

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Data availability

Next-generation sequencing data generated in this study has been uploaded to the National Genomic Data Center (https://ngdc.cncb.ac.cn/, #HRA008275). Previously published bulk ATAC/RNA-seq and scRNA-seq data of ATRA-treated NB4 cells [14] are publicly available from The National Omics Data Encyclopedia (https://www.biosino.org/node, #OEP001921).

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Acknowledgements

This study is supported by research funding from the National Natural Science Foundation of China (81970130 and 81770143), National Key Research and Development Program of China (2018YFA0107802), Shanghai Commission of Science and Technology (17PJ1405800), Shanghai Municipal Education Commission Gaofeng Clinical Medicine Grant (20171902), and Shanghai Dong Fang Scholarship. The computations in this paper were performed on the ASTRA High Performance Computing Cluster supported by the National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

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Author notes

  1. These authors contributed equally: Xin Tian, Liuqingqing Zhang, Guiqiyang Xiang.

Authors and Affiliations

  1. 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

    Xin Tian,Ā Liuqingqing Zhang,Ā Guiqiyang Xiang,Ā Yijia Tang,Ā Ping Zhu,Ā Shuting Yu,Ā Fangying Jiang,Ā Shuai Wang,Ā Jinzeng Wang,Ā Yao Dai,Ā Xiangqin Weng,Ā Shengyue Wang,Ā Yun TanĀ &Ā Feng Liu

  2. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China

    Liuqingqing Zhang

  3. School of Computer Science, Southwest Petroleum University, Chengdu, China

    Desheng Zheng

  4. Clinical Laboratory, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China

    Jianbiao Wang

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Contributions

FL conceived and supervised the study. XT, LQQZ, GQYX, YJT, PZ, STY, FYJ, SW, YD, JZW, and XQW performed experiments and data analysis. DSZ, HL, JBW, SYW, and YT analyzed the data. FL, XT, and LQQZ wrote the paper with comments from all other authors.

Corresponding author

Correspondence to Feng Liu.

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The authors declare no competing interests.

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Patient samples were obtained according to the Declaration of Helsinki. Informed consent was obtained from all participants according to the procedures approved by the Institutional Review Board of Ruijin Hospital, which is affiliated with Shanghai Jiao Tong University School of Medicine (No. 2023-LLDS-355).

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Tian, X., Zhang, L., Xiang, G. et al. Single-cell multiomics reveals a gene regulatory circuit driving leukemia cell differentiation. Oncogene 44, 1350ā€“1360 (2025). https://doi.org/10.1038/s41388-025-03309-z

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