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Hypoxic stabilization of RIPOR3 mRNA via METTL3-mediated m6A methylation drives breast cancer progression and metastasis

Oncogene volume 43, pages 3426–3441 (2024)Cite this article

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Abstract

Dysregulated N6-methyladenosine (m6A) modification has been associated with breast cancer pathogenesis. Hypoxia which characterizes solid tumors is known to reprogram the m6A epitranscriptome, but the underlying mechanisms of how this process contributes to breast cancer progression remain poorly understood. Through integrative analyses of m6A-RIP sequencing and RNA sequencing databases, we reveal a cluster of mRNAs with upregulated m6A methylation and expression under hypoxia, that are enriched by many oncogenic pathways, including PI3K–Akt signaling. Furthermore, we identify the mRNA, RIPOR3, as a target of METTL3-mediated m6A methylation in response to hypoxia. We find that m6A methylation stabilizes RIPOR3, increasing its protein expression in a METTL3 catalytic activity-dependent manner, and consequently driving breast tumor growth and metastasis. RIPOR3 is found to be overexpressed in breast cancer cell lines and tumor tissues from breast cancer patients, in whom elevated RIPOR3 is associated with a worse prognosis. Mechanistically, we show that RIPOR3 interacts with EGFR and is essential for the PI3K–Akt pathway activation. In conclusion, we identify RIPOR3 as a hypoxia-stabilized oncogenic driver via METTL3-mediated m6A methylation, thus provide a potential therapeutic target for breast cancer.

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Fig. 1: Integrative analyses of m6A-RIP sequencing and RNA sequencing data reveal a set of hypoxia-increased mRNA with elevated m6A methylation that are enriched by oncogenic pathways.
Fig. 2: Identification of RIPOR3 as a hypoxia-stabilized mRNA via METTL3-mediated m6A methylation.
Fig. 3: RIPOR3 is involved in breast cancer pathogenesis.
Fig. 4: RIPOR3 accelerates breast tumor growth.
Fig. 5: RIPOR3 promotes breast cancer cells metastasis.
Fig. 6: RIPOR3 is an important target of METTL3 in driving breast cancer cell growth and metastasis.
Fig. 7: RIPOR3 is required for the EGFR–PI3K–Akt pathway activation.
Fig. 8: RIPOR3 promotes breast cancer cell proliferation, migration and invasion through the EGFR and Akt activation.

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Data availability

The m6A-seq data have been deposited in the GEO repository under the accession numbers GEO: GSE264247 and GSE264245. The RNA-seq data have been deposited in the GEO repository under the accession number GEO: GSE263916. The IP–MS data have been deposited to the ProteomeXchange Consortium via the iProX repository with the data set identifier IPX0009452001 (URL:https://www.iprox.cn/page/SSV024.html;url=1723740855494Zi2E).

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Acknowledgements

The authors thank members of our laboratory for helpful discussions. We thank Dr. Haojian Zhang (Wuhan University) for providing critical plasmids. We also sincerely thank the core facility of the Medical Research Institute at Wuhan University for their wonderful technical support.

Funding

This work is supported by the National Key Research and Development Program of China 2022YFA1305400 (JZ), the National Natural Science Foundation of China 32370762 (JZ) and 32100570 (CY), the Natural Science Foundation of Hubei Province of China 2022CFA008 (JZ), and the Fundamental Research Funds for the Central Universities 2042022dx0003 (JZ).

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Author notes

  1. These authors contributed equally: Jingjing Xiong, Zirui Zhou, Yulong Jiang.

Authors and Affiliations

  1. Department of Urology, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China

    Jingjing Xiong, Zirui Zhou, Yulong Jiang, Qifang Li, Jiahao Guo, Chaojun Yan & Jing Zhang

  2. Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China

    Zuhan Geng

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  1. Jingjing Xiong
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  2. Zirui Zhou
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Contributions

JZ conceived and supervised the project. JX performed most of the experiments and analyzed the data. ZZ helped with most of the Q-PCR assays and m6A dot blot assays. YJ performed most of the bioinformatics analyses. QL performed some of those Co-IP and WB assays. QL, ZG, JG and ZZ helped with animal experiments. CY constructed some of those plasmids and prepared samples for m6A-RIP sequencing and RNA sequencing. JZ, CY and JX wrote the paper with critical comments from all authors.

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Correspondence to Chaojun Yan or Jing Zhang.

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Xiong, J., Zhou, Z., Jiang, Y. et al. Hypoxic stabilization of RIPOR3 mRNA via METTL3-mediated m6A methylation drives breast cancer progression and metastasis. Oncogene 43, 3426–3441 (2024). https://doi.org/10.1038/s41388-024-03180-4

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