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YBX1 promotes 5-Fluorouracil resistance in gastric cancer via m5C-dependent ATG9A mRNA stabilization through autophagy

Oncogene volume 44, pages 2357–2371 (2025)Cite this article

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Abstract

5-Fluorouracil (5-FU) is a first-line chemotherapeutic agent for advanced gastric cancer (GC). However, its clinical efficacy is often undermined by the development of chemoresistance. Aberrant activation of oncogenic pathways, including autophagy, has been implicated in 5-FU resistance. Epigenetic modifications, such as 5-methylcytosine (m5C), are also recognized to modulate autophagy and contribute to chemoresistance, though the underlying molecular mechanisms remain poorly understood. In this study, we discovered that YBX1, an m5C reader protein, was significantly upregulated in 5-FU-resistant GC cell lines and patient tissues. Both in vitro and in vivo experiments demonstrated that YBX1 promoted autophagy in GC cells, thereby enhancing 5-FU resistance. Mechanistically, the transcription factor MAZ was found to bind to the YBX1 promoter, driving its transcriptional upregulation. YBX1, in turn, stabilized ATG9A mRNA via NSUN2-mediated m5C modification, thereby enhancing autophagic activity and conferring chemoresistance. Clinically, elevated YBX1 expression correlated with poor prognosis in patients with advanced GC undergoing 5-FU-based chemotherapy. These findings establish YBX1 as a key regulator of autophagy and 5-FU resistance in GC and highlight its potential as a novel therapeutic target for overcoming 5-FU resistance.

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Fig. 1: YBX1 is upregulated in 5-FU resistant GC cell lines and tissues.
Fig. 2: YBX1 enhances 5-FU resistance in AGS cells without affecting proliferation.
Fig. 3: Transcriptional factor MAZ promotes YBX1 expression in GC cells.
Fig. 4: YBX1 enhances 5-FU resistance by inducing protective autophagy in vitro and in vivo.
Fig. 5: YBX1 stabilizes ATG9A mRNA in an m5C-dependent manner.
Fig. 6: NSUN2-mediated m5C modification of ATG9A maintains its stability.
Fig. 7: YBX1 promotes autophagy and 5-FU resistance in GC by upregulating ATG9A expression.
Fig. 8: YBX1 is a prognostic indicator in GC patients receiving 5-FU-based adjuvant chemotherapy.

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Data availability

All data supporting the findings of this study are available in the manuscript and its supplementary materials. Additional data and codes can be requested from the corresponding author.

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Acknowledgements

We would like to thank the Core Facility of the First Affiliated Hospital of Nanjing Medical University for its help in the detection of experimental samples. All experimental design schemes were created with FigureDraw. This work was partially supported by the National Natural Science Foundation of China (82273038, 82072708); Special Foundation for National Science and Technology Basic Research Program of China (2019FY101104); Jiangsu Province Capability Improvement Project through Science, Technology and Education (Jiangsu Provincial Medical Key Discipline, ZDXK202222); the Program for Development of Innovative Research Team in the First Affiliated Hospital of NJMU, the Priority Academic Program Development of Jiangsu Higher Education Institutions (JX10214177, JX10231801); Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University.

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Author notes

  1. These authors contributed equally: Hongxin Huang, Lang Fang, Chuming Zhu, Jialun Lv.

Authors and Affiliations

  1. Gastric Cancer Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, China

    Hongxin Huang, Lang Fang, Chuming Zhu, Jialun Lv, Penghui Xu, Zetian Chen, Zhijun Zhang, Jihuan Wang, Weizhi Wang & Zekuan Xu

  2. Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, China

    Hongxin Huang, Lang Fang, Chuming Zhu, Jialun Lv, Penghui Xu, Zetian Chen, Zhijun Zhang, Jihuan Wang, Weizhi Wang & Zekuan Xu

  3. Institute for Gastric Cancer Research, Nanjing Medical University, Nanjing, Jiangsu, 211166, China

    Zekuan Xu

  4. Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China

    Zekuan Xu

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Contributions

Hongxin Huang and Lang Fang contributed to experimental design and data analysis. Chuming Zhu and Jialun Lv conducted several in vitro experiments. Penghui Xu and Zetian Chen provided guidance for animal studies. Zhijun Zhang and Jihuan Wang assisted with bioinformatics analysis. Hongxin Huang drafted the manuscript. Weizhi Wang and Zekuan Xu were responsible for quality control. All authors reviewed and approved the final manuscript.

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Correspondence to Weizhi Wang or Zekuan Xu.

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The authors declare no competing financial interests or personal relationships that could have influenced the research presented in this paper.

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Gastric cancer patient specimens were collected under the approval of the Ethics Committee of the First Affiliated Hospital of Nanjing Medical University. Written informed consent was obtained from each patient for the use of their tissue samples. All animal experiments were conducted in compliance with protocols approved by the Ethics Committee of Nanjing Medical University.

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Huang, H., Fang, L., Zhu, C. et al. YBX1 promotes 5-Fluorouracil resistance in gastric cancer via m5C-dependent ATG9A mRNA stabilization through autophagy. Oncogene 44, 2357–2371 (2025). https://doi.org/10.1038/s41388-025-03411-2

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