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ZNF689 deficiency promotes intratumor heterogeneity and immunotherapy resistance in triple-negative breast cancer

Cell Research volume 34, pages 58–75 (2024)Cite this article

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Abstract

Triple-negative breast cancer (TNBC) is an aggressive disease characterized by remarkable intratumor heterogeneity (ITH), which poses therapeutic challenges. However, the clinical relevance and key determinant of ITH in TNBC are poorly understood. Here, we comprehensively characterized ITH levels using multi-omics data across our center’s cohort (n = 260), The Cancer Genome Atlas cohort (n = 134), and four immunotherapy-treated cohorts (n = 109). Our results revealed that high ITH was associated with poor patient survival and immunotherapy resistance. Importantly, we identified zinc finger protein 689 (ZNF689) deficiency as a crucial determinant of ITH formation. Mechanistically, the ZNF689–TRIM28 complex was found to directly bind to the promoter of long interspersed element-1 (LINE-1), inducing H3K9me3-mediated transcriptional silencing. ZNF689 deficiency reactivated LINE-1 retrotransposition to exacerbate genomic instability, which fostered ITH. Single-cell RNA sequencing, spatially resolved transcriptomics and flow cytometry analysis confirmed that ZNF689 deficiency-induced ITH inhibited antigen presentation and T-cell activation, conferring immunotherapy resistance. Pharmacological inhibition of LINE-1 significantly reduced ITH, enhanced antitumor immunity, and eventually sensitized ZNF689-deficient tumors to immunotherapy in vivo. Consistently, ZNF689 expression positively correlated with favorable prognosis and immunotherapy response in clinical samples. Altogether, our study uncovers a previously unrecognized mechanism underlying ZNF689 deficiency-induced ITH and suggests LINE-1 inhibition combined with immunotherapy as a novel treatment strategy for TNBC.

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Fig. 1: High ITH reduces patient survival and confers immunotherapy resistance in TNBC.
Fig. 2: ZNF689 deficiency promotes ITH in TNBC.
Fig. 3: ZNF689 represses LINE-1 retrotransposition via TRIM28 complex-mediated transcriptional silencing.
Fig. 4: ZNF689 deficiency-induced LINE-1 retrotransposition exacerbates genomic instability and promotes ITH.
Fig. 5: ZNF689 deficiency-induced ITH impairs antigen presentation and T-cell activation.
Fig. 6: LINE-1 inhibition sensitizes ZNF689 deficiency-induced high-ITH tumors to immunotherapy in TNBC.
Fig. 7: ZNF689 expression positively correlates with a favorable prognosis and immunotherapy response in TNBC.

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Data availability

Sequence data have been deposited in the NCBI Gene Expression Omnibus (OncoScan array; GEO: GSE118527) and Sequence Read Archive (WES and RNA-seq; SRA: SRP157974). Other data that support the findings of this study are presented in the main text and in the online Supplementary information. Sequencing coverage for our datasets is detailed in Supplementary information, Table S10, while quality control metrics are provided in Supplementary information, Table S11. Further information and requests for resources and reagents should be directed to and will be fulfilled by the corresponding authors.

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Acknowledgements

We thank Hong-Jie Shen, Wen-Qi Xu and Jin Wang from the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, for their expert guidance on the regulatory mechanism of ZNF689 on LINE-1. This work was supported by the National Key R&D Program of China (2020YFA0112304), the National Natural Science Foundation of China (82272822, 81922048, 82341003, 82002799 and 92159301), the Natural Science Foundation of Shanghai (22ZR1479200 and 23ZR1411800), the Shanghai Key Laboratory of Breast Cancer (12DZ2260100), the SHDC Municipal Project for Developing Emerging and Frontier Technology in Shanghai Hospitals (SHDC12021103) and the Youth Talent Program of Shanghai Health Commission (2022YQ012).

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  1. These authors contributed equally: Li-Ping Ge, Xi Jin, Ding Ma, Zi-Yu Wang.

Authors and Affiliations

  1. Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China

    Li-Ping Ge, Xi Jin, Ding Ma, Zi-Yu Wang, Cheng-Lin Liu, Chao-Zheng Zhou, Shen Zhao, Tian-Jian Yu, Xi-Yu Liu, Gen-Hong Di, Zhi-Ming Shao & Yi-Zhou Jiang

  2. Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China

    Li-Ping Ge, Xi Jin, Ding Ma, Zi-Yu Wang, Cheng-Lin Liu, Chao-Zheng Zhou, Shen Zhao, Tian-Jian Yu, Xi-Yu Liu, Gen-Hong Di, Zhi-Ming Shao & Yi-Zhou Jiang

  3. Human Phenome Institute, Fudan University, Shanghai, China

    Li-Ping Ge & Zhi-Ming Shao

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Contributions

Y.-Z.J., Z.-M.S. and G.-H.D. conceived the research project. Z.-M.S. and Y.-Z.J. secured funding and supervised the study. L.-P.G. designed and performed most experiments, analyzed the data, and wrote the manuscript. X.J. designed the experiments and supervised the study. D.M., Z.-Y.W., C.-L.L. and X.-Y.L performed the bioinformatics analyses. C.-Z.Z, S.Z. and T.-J.Y. assisted with flow cytometry and histology imaging. Y.-Z.J., L.-P.G., X.J., D.M., Z.-Y.W. and S.Z. discussed the results and manuscript. All authors have read and approved the manuscript.

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Correspondence to Gen-Hong Di, Zhi-Ming Shao or Yi-Zhou Jiang.

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Ge, LP., Jin, X., Ma, D. et al. ZNF689 deficiency promotes intratumor heterogeneity and immunotherapy resistance in triple-negative breast cancer. Cell Res 34, 58–75 (2024). https://doi.org/10.1038/s41422-023-00909-w

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  • DOI: https://doi.org/10.1038/s41422-023-00909-w

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