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ZDHHC20-mediated S-palmitoylation of KAP1/TRIM28 promotes DNA damage repair

Oncogene volume 44, pages 4533–4548 (2025)Cite this article

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Abstract

S-palmitoylation mediated by the zinc finger aspartate-histidine-histidine-cysteine (ZDHHC) protein acyltransferases (PATs) modulates protein localization, stability, interactions and signal transduction. In this study, we screened the 23 ZDHHC family members and identified ZDHHC20 as one of the major PATs involved in the DNA damage response (DDR). Inhibition of ZDHHC20 expression impaired cellular DNA damage repair capabilities. Meanwhile, data from ZDHHC20 knock-out mice, human tumor cell lines and xenograft tumor models showed that knock-out of ZDHHC20 significantly enhanced radiosensitivity. Using palmitoylation label-free quantitative proteomics, we found that over 600 proteins were palmitoylated in a ZDHHC20-dependent manner. Via the acyl-biotin exchange (ABE) assay, we revealed that KRAB-associated protein 1 (KAP1), also known as tripartite motif-containing protein 28 (Trim28), was palmitoylated at cysteine 232 by ZDHHC20. Notably, ZDHHC20-dependent KAP1 palmitoylation increased the chromatin binding of phosphorylated KAP1, which facilitated chromatin accessibility and subsequent recruitment of the DDR components BRCA1 and 53BP1. Further, we demonstrated that Ataxia-Telangiectasia Mutated (ATM)-dependent phosphorylation of ZDHHC20 at serine 339 increased KAP1 palmitoylation. Taken together, our findings elucidate the role and mechanism of the ATM-ZDHHC20-KAP1 axis in the DDR and provide a novel sensitizing strategy for radiotherapy and chemotherapy.

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Fig. 1: ZDHHC20 is one of the key ZDHHC palmitoyl transferases that is prominently involved in the DDR.
Fig. 2: ZDHHC20 regulates radiosensitivity and DNA damage repair.
Fig. 3: ZDHHC20 promotes the palmitoylation of the chromatin remodeling factor KAP1.
Fig. 4: Depletion of ZDHHC20 weakens the regulation of KAP1 in the DDR.
Fig. 5: KAP1 C232S leads to defects in DNA damage repair in tumor cells.
Fig. 6: DNA damage-induced ATM-dependent phosphorylation of ZDHHC20 at S339 promotes the palmitoylation of KAP1.
Fig. 7: The ZDHHC20 S339A mutation inhibits DNA damage repair and increases the radiosensitivity of tumor cells.
Fig. 8

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All relevant data generated in this study are available within the article and supplementary files.

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China [82272754, 82503164, 82003237]; Chongqing University Educational Reform Research Project [2021Y55]; China Postdoctoral Science Foundation [grant number 2024M752392]; The Scientific Research Project of Tianjin Education Commission [grant number 2022KJ220]; The Natural Science Foundation of Shanghai (25ZR1402085); Tianjin Medical University Cancer Institute and Hospital Innovation Fund [grant number B2203]; Tianjin Key Medical Discipline Construction Project [grant number TJYXZDXK-3-004B]. We appreciate Dr. Lei Shi for providing relevant cell lines.

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  1. These authors contributed equally: Zhuang Liu, Han Wang, Yamei Han.

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, The Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China

    Zhuang Liu, Yamei Han, Yang Chen, Youyou Wang, Siyue Zhang, Mingming Xiao & Bo Xu

  2. Department of Head and Neck Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, China

    Zhuang Liu

  3. Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Chongqing University Cancer Hospital and Chongqing University School of Medicine, Chongqing, China

    Han Wang, Yaqi Mo, Chuanjie Wang & Bo Xu

  4. Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China

    Mingming Xiao

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Contributions

ZL, HW, and YH performed most of the experiments and wrote the manuscript. YC, YW, SZ, YM, CW, and MX performed experiments and analyzed the data. BX and MX conceived the study and experimental design and revised the manuscript.

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Correspondence to Mingming Xiao or Bo Xu.

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Liu, Z., Wang, H., Han, Y. et al. ZDHHC20-mediated S-palmitoylation of KAP1/TRIM28 promotes DNA damage repair. Oncogene 44, 4533–4548 (2025). https://doi.org/10.1038/s41388-025-03604-9

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