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METTL3 promotes cellular senescence of colorectal cancer via modulation of CDKN2B transcription and mRNA stability

Oncogene volume 43, pages 976–991 (2024)Cite this article

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Abstract

Cellular senescence plays a critical role in cancer development, but the underlying mechanisms remain poorly understood. Our recent study uncovered that replicative senescent colorectal cancer (CRC) cells exhibit increased levels of mRNA N6-methyladenosine (m6A) and methyltransferase METTL3. Knockdown of METTL3 can restore the senescence-associated secretory phenotype (SASP) of CRC cells. Our findings, which were confirmed by m6A-sequencing and functional studies, demonstrate that the cyclin-dependent kinase inhibitor 2B (CDKN2B, encoding p15INK4B) is a mediator of METTL3-regulated CRC senescence. Specifically, m6A modification at position A413 in the coding sequence (CDS) of CDKN2B positively regulates its mRNA stability by recruiting IGF2BP3 and preventing binding with the CCR4-NOT complex. Moreover, increased METTL3 methylates and stabilizes the mRNA of E2F1, which binds to the −208 to −198 regions of the CDKN2B promoter to facilitate transcription. Inhibition of METTL3 or specifically targeting CDKN2B methylation can suppress CRC senescence. Finally, the METTL3/CDKN2B axis-induced senescence can facilitate M2 macrophage polarization and is correlated with aging and CRC progression. The involvement of METTL3/CDKN2B in cell senescence provides a new potential therapeutic target for CRC treatment and expands our understanding of mRNA methylation’s role in cellular senescence.

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Fig. 1: METTL3 regulates culture-related replicative senescence of CRC cells.
Fig. 2: CDKN2B (p15INK4b) mediates METTL3-regulated senescence of CRC cells.
Fig. 3: METTL3 increases mRNA stability and transcription of CDKN2B in senescent CRC cells.
Fig. 4: IGF2BP3 stabilizes CDKN2B mRNA via binding with m6A 413 at CDS.
Fig. 5: METTL3 increases transcription of CDKN2B via E2F1.
Fig. 6: Generally or specifically targeting m6A suppresses CRC senescence.
Fig. 7: m6A-induced senescent CRC cells facilitates the M2 macrophage polarization.
Fig. 8: METTL3/CDKN2B-regualted senescence correlates with aging, CRC progression and TAM infiltration.

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Data availability

m6A-seq data are available through SRA, PRJNA841050. The detailed procedures of methods, eight figures and four tables are attached. All study data are included in the article and/or Supplementary materials.

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Acknowledgements

We thank Prof Hao Liu at the Cancer Center of Guangzhou Medical University for plasmid donation, experimental skills and instrumental help.

Funding

This research was supported by the National Key Research and Development Program of China (No. 2022YFC2601800, and 2022YFC3401000), the National Natural Science Foundation of China (Nos. 32161143017, 82173833, 82372743, 82173126, 81973343, 82272658, 82373893, and 82022037), the Guangdong Basic and Applied Basic Research Foundation (Nos. 2023B1515040006, and 2021B1515230009), the Open Program of Shenzhen Bay Laboratory (No. SZBL202009051006), the Guangdong Provincial Key Laboratory of Construction Foundation (2023B1212060022), the Guangdong Provincial Natural Science Foundation (2019B151502063), the Sichuan Science and Technology Program (Nos. 2022JDRC0042, and 2022NSFSC0776), the Joint Research Foundation of Chengdu Medical College and the Seventh People’s Hospital (Grant Nos. 2022LHTD-02, 2021LHJYPJ-08 and 2022488), and the Shenzhen Bay Scholars Program.

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  1. These authors contributed equally: Zhuojia Chen, Jiawang Zhou, You Wu, Feng Chen.

Authors and Affiliations

  1. Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China

    Zhuojia Chen

  2. Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China

    Jiawang Zhou, You Wu, Feng Chen, Jianing Li, Lijun Tao, Yifan Tian, Haoran Wang, Jiexin Li & Hongsheng Wang

  3. Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518067, China

    Zigang Li

  4. Department of Gastrointestinal Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361000, Fujian, China

    Weiling He

  5. The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu Seventh People’s Hospital, Affiliated Cancer Hospital of Chengdu Medical College, School of Biological Sciences and Technology, Chengdu Medical College, Chengdu, 610500, China

    Kun Zhang

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Contributions

HS Wang, ZJ Chen, ZG Li, Q Peng, W He, and JX Li designed and initiated the study; Y Wu, F Chen, JW Zhou, K Zhong, and HR Wang performed experiments; HS Zhang, JN Li, LJ Tao, and YF Tian helped design the study and interpret the data; ZJ Chen and HS Wang wrote the paper.

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Correspondence to Weiling He, Kun Zhang or Hongsheng Wang.

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Chen, Z., Zhou, J., Wu, Y. et al. METTL3 promotes cellular senescence of colorectal cancer via modulation of CDKN2B transcription and mRNA stability. Oncogene 43, 976–991 (2024). https://doi.org/10.1038/s41388-024-02956-y

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