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N4-acetylcytidine modification of lncRNA CTC-490G23.2 promotes cancer metastasis through interacting with PTBP1 to increase CD44 alternative splicing

Oncogene volume 42, pages 1101–1116 (2023)Cite this article

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Abstract

Although N4-acetylcytidine (ac4C) modification affects the stability and translation of mRNA, it is unknown whether it exists in noncoding RNAs, and its biological function is unclear. Here, nucleotide-resolution method for profiling CTC-490G23.2 ac4C sites and gain- and loss-of-function experiments revealed that N-acetyltransferase 10 (NAT10) is responsible for ac4C modification of long noncoding RNAs (lncRNAs). NAT10-mediated ac4C modification leads to the stabilization and overexpression of lncRNA CTC-490G23.2 in primary esophageal squamous cell carcinoma (ESCC) and its further upregulation in metastatic tissues. CTC-490G23.2 significantly promotes cancer invasion and metastasis in vitro and in vivo. Mechanistically, CTC-490G23.2 acts as a scaffold to increase the binding of CD44 pre-mRNA to polypyrimidine tract-binding protein 1 (PTBP1), resulting in a oncogenic splicing switch from the standard isoform CD44s to the variant isoform CD44v(8-10). CD44v(8-10), but not CD44s, binds to and increases the protein stability of vimentin. Expression levels of CTC-490G23.2 and CD44v(8-10) can predict poor prognosis in cancer patients. Furthermore, the antisense oligonucleotide (ASO)/SV40-LAH4-L1 peptide self-assembled nanocomplexes targeting CTC490G23.2 exerts a significantly suppressive effect on cancer metastasis. The outcome of this study will provide new mechanistic insight into the ac4C modification of lncRNAs and useful clues for the development of novel systemic therapies and prognostic biomarkers.

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Fig. 1: NAT10-mediated ac4C modification increases CTC-490G23.2 stability in esophageal cancer.
Fig. 2: Upregulation of CTC-490G23.2 in ESCC promotes tumor metastasis.
Fig. 3: PTBP1 is a binding protein and an important effector of CTC-490G23.2.
Fig. 4: CTC-490G23.2 binds to both PTBP1 and CD44 pre-mRNA to increase their interaction.
Fig. 5: PTBP1-induced alternative splicing of CD44 mediates the role of CTC-490G23.2 in promoting cancer metastasis.
Fig. 6: CD44v(8-10) specifically binds to vimentin and increases its stability.
Fig. 7: Targeting CTC-490G23.2 with ASO nanocomplexes suppresses metastasis in esophageal cancer.
Fig. 8: An overview of CTC-490G23.2 function.

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Data availability

All data needed to evaluate the conclusions presented in the article are available in the article and/or the Supplementary Materials. Sequencing data have been deposited in Gene Expression Omnibus with the accession GSE212716. Mass spectrometry data have been deposited in proteomeXchange with the accession PXD036513, PXD036524 and PXD036537.

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Acknowledgements

We thank Professor Didier Trono and Professor Vladislav Verkhusha for the plasmids obtained from Addgene.

Funding

This work was supported by National Key Research and Development Program of China (2021YFC2501000, 2021YFC2501900), National Natural Science Foundation of China (82073196, 82273141, 31961160727, 81973339), Natural Science Foundation of Guangdong Province (2021A1515011158, 2021A0505030035), and Key Laboratory of Guangdong Higher Education Institutes (2021KSYS009).

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Author notes

  1. These authors contributed equally: Xiao-Mei Yu, Shu-Jun Li, Zi-Ting Yao, Jiao-Jiao Xu.

Authors and Affiliations

  1. Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China

    Xiao-Mei Yu, Shu-Jun Li, Jiao-Jiao Xu, Can-Can Zheng, Peng-Bo Ding, Xian Wei, Lin-Ping Zhao & Bin Li

  2. MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China

    Xiao-Mei Yu, Shu-Jun Li, Zi-Ting Yao, Jiao-Jiao Xu & Peng-Bo Ding

  3. Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China

    Zhi-Chao Liu & Zhi-Gang Li

  4. Department of Radiation Oncology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China

    Zhi-Li Jiang & Xing-Yuan Shi

  5. Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China

    Wen Wen Xu

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Contributions

XMY, SJL, ZTY and JJX: acquisition of data, analysis and interpretation of data, statistical analysis, drafting of the manuscript; CCZ, PBD, ZLJ, XW, LPZ and XYS: acquisition of data, analysis and interpretation of data; ZCL and ZGL: technical and/or material support; WWX: funding acquisition, technical and/or material support and critical revision of the manuscript for important intellectual content; BL: funding acquisition, study concept and design, study supervision. All authors edited and approved the final version of the manuscript.

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Correspondence to Bin Li.

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The authors declare no competing interests.

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All animal experiments were approved by the experimental Animal Ethics Committee of Guangzhou Medical University and performed according to institutional guidelines. Biospecimens were collected from newly diagnosed patients who underwent surgical resection (Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China). All sample collection procedures complied with routine clinical practice.

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Yu, XM., Li, SJ., Yao, ZT. et al. N4-acetylcytidine modification of lncRNA CTC-490G23.2 promotes cancer metastasis through interacting with PTBP1 to increase CD44 alternative splicing. Oncogene 42, 1101–1116 (2023). https://doi.org/10.1038/s41388-023-02628-3

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