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METTL3-mediated m6A modification of lncRNA TSPAN12 promotes metastasis of hepatocellular carcinoma through SENP1-depentent deSUMOylation of EIF3I

Abstract

In a previous study, we discovered that the level of lnc-TSPAN12 was significantly elevated in hepatocellular carcinoma (HCC) and correlated with a low survival rate. However, the function and mechanism of lnc-TSPAN12 in modulating epithelial-mesenchymal transition (EMT) and metastasis in HCC remains poorly understood. This study demonstrates that lnc-TSPAN12 positively influences migration, invasion, and EMT of HCC cells in vitro and promotes hepatic metastasis in vivo. The modification of N6-methyladenosine, driven by METTL3, is essential for the stability of lnc-TSPAN12, which may partially contribute to the upregulation of lnc-TSPAN12. Mechanistically, lnc-TSPAN12 exhibits direct interactions with EIF3I and SENP1, acting as a scaffold to enhance the SENP1-EIF3I interaction. As a result, the SUMOylation of EIF3I is inhibited, preventing its ubiquitin-mediated degradation. Ultimately, this activates the Wnt/β-catenin signaling pathway, stimulating EMT and metastasis in HCC. Our findings shed light on the regulatory mechanism of lnc-TSPAN12 in HCC metastasis and identify the lnc-TSPAN12-EIF3I/SENP1 axis as a novel therapeutic target for HCC.

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Fig. 1: Lnc-TSPAN12 promotes migration, invasion and EMT of HCC cells in vitro.
Fig. 2: Lnc-TSPAN12 promotes metastasis in HCC.
Fig. 3: Lnc-TSPAN12 physically interacts with EIF3I and SENP1.
Fig. 4: Lnc-TSPAN12 enhances the stability of EIF3I protein by blocking its ubiquitination degradation.
Fig. 5: Lnc-TSPAN12 knockdown promotes EIF3I ubiquitination through suppressing SENP1-mediated deSUMOylation.
Fig. 6: Lnc-TSPAN12 exerts EMT-promoting functions in HCC by regulating EIF3I/SENP1.
Fig. 7: Lnc-TSPAN12 is upregulated in HCC through METTL3-mediated m6A modification.
Fig. 8

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Data availability

The data in this study are available upon request from the corresponding author.

References

  1. Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71:209–49.

    Article  PubMed  Google Scholar 

  2. Kulik L, El-Serag HB. Epidemiology and management of hepatocellular carcinoma. Gastroenterology. 2019;15:477–91.e1.

    Article  Google Scholar 

  3. Yao RW, Wang Y, Chen LL. Cellular functions of long noncoding RNAs. Nat Cell Biol. 2019;21:542–51.

    Article  CAS  PubMed  Google Scholar 

  4. Postepska-Igielska A, Giwojna A, Gasri-Plotnitsky L, Schmitt N, Dold A, Ginsberg D, et al. LncRNA Khps1 regulates expression of the proto-oncogene SPHK1 via triplex-mediated changes in chromatin structure. Mol Cell. 2015;60:626–36.

    Article  CAS  PubMed  Google Scholar 

  5. Lee S, Kopp F, Chang TC, Sataluri A, Chen B, Sivakumar S, et al. Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell. 2016;164:69–80.

    Article  CAS  PubMed  Google Scholar 

  6. Liu B, Sun L, Liu Q, Gong C, Yao Y, Lv X, et al. A cytoplasmic NF-κB interacting long noncoding RNA blocks IκB phosphorylation and suppresses breast cancer metastasis. Cancer Cell. 2015;27:370–81.

    Article  CAS  PubMed  Google Scholar 

  7. Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet. 2015;47:199–208.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Huarte M. The emerging role of lncRNAs in cancer. Nat Med. 2015;21:1253–61.

    Article  CAS  PubMed  Google Scholar 

  9. Liu SJ, Dang HX, Lim DA, Feng FY, Maher CA. Long noncoding RNAs in cancer metastasis. Nat Rev Cancer. 2021;21:446–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Huang Z, Zhou JK, Peng Y, He W, Huang C. The role of long noncoding RNAs in hepatocellular carcinoma. Mol Cancer. 2020;19:77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Dongre A, Weinberg RA. New insights into the mechanisms of epithelial-mesenchymal transition and implications for cancer. Nat Rev Mol Cell Biol. 2019;20:69–84.

    Article  CAS  PubMed  Google Scholar 

  12. Lu M, Zhu WW, Wang X, Tang JJ, Zhang KL, Yu GY, et al. ACOT12-dependent alteration of acetyl-CoA drives hepatocellular carcinoma metastasis by epigenetic induction of epithelial-mesenchymal transition. Cell Metab. 2019;29:886–900.

    Article  CAS  PubMed  Google Scholar 

  13. Krebs AM, Mitschke J, Lasierra Losada M, Schmalhofer O, Boerries M, Busch H, et al. The EMT-activator Zeb1 is a key factor for cell plasticity and promotes metastasis in pancreatic cancer. Nat Cell Biol. 2017;19:518–29.

    Article  CAS  PubMed  Google Scholar 

  14. Shibue T, Weinberg RA. EMT, CSCs, and drug resistance: the mechanistic link and clinical implications. Nat Rev Clin Oncol. 2017;14:611–29.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Grelet S, Link LA, Howley B, Obellianne C, Palanisamy V, Gangaraju VK, et al. A regulated PNUTS mRNA to lncRNA splice switch mediates EMT and tumour progression. Nat Cell Biol. 2017;19:1105–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Wang YQ, Jiang DM, Hu SS, Zhao L, Wang L, Yang MH, et al. SATB2-AS1 suppresses colorectal carcinoma aggressiveness by inhibiting SATB2-dependent snail transcription and epithelial-mesenchymal transition. Cancer Res. 2019;79:3542–56.

    Article  CAS  PubMed  Google Scholar 

  17. Roundtree IA, Evans ME, Pan T, He C. Dynamic RNA modifications in gene expression regulation. Cell. 2017;169:1187–200.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Yang Y, Hsu PJ, Chen YS, Yang YG. Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism. Cell Res. 2018;28:616–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Huang H, Weng H, Chen J. M6A modification in coding and non-coding RNAs: roles and therapeutic implications in cancer. Cancer Cell. 2020;37:270–88.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Wang Q, Chen C, Ding Q, Zhao Y, Wang Z, Chen J, et al. METTL3-mediated m6A modification of HDGF mRNA promotes gastric cancer progression and has prognostic significance. Gut. 2020;69:1193–205.

    Article  CAS  PubMed  Google Scholar 

  21. Lu J, Li B, Xiong X, Cheng N. RNA sequencing reveals the long noncoding RNA and mRNA profiles and identifies long non-coding RNA TSPAN12 as a potential microvascular invasion-related biomarker in hepatocellular carcinoma. Biomed Pharmacother. 2020;126:110111.

    Article  CAS  PubMed  Google Scholar 

  22. Zhang C, Wei S, Sun WP, Teng K, Dai MM, Wang FW, et al. Super-enhancer-driven AJUBA is activated by TCF4 and involved in epithelial-mesenchymal transition in the progression of Hepatocellular Carcinoma. Theranostics. 2020;10:9066–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Yuan K, Xie K, Lan T, Xu L, Chen X, Li X, et al. TXNDC12 promotes EMT and metastasis of hepatocellular carcinoma cells via activation of β-catenin. Cell Death Differ. 2020;27:1355–68.

    Article  CAS  PubMed  Google Scholar 

  24. Qi J, Dong Z, Liu J, Zhang JT. EIF3I promotes colon oncogenesis by regulating COX-2 protein synthesis and β-catenin activation. Oncogene. 2014;33:4156–63.

    Article  CAS  PubMed  Google Scholar 

  25. Wang YW, Lin KT, Chen SC, Gu DL, Chen CF, Tu PH, et al. Overexpressed-EIF3I interacted and activated oncogenic Akt1 is a theranostic target in human hepatocellular carcinoma. Hepatology. 2013;58:239–50.

    Article  CAS  PubMed  Google Scholar 

  26. Agostini F, Zanzoni A, Klus P, Marchese D, Cirillo D, Tartaglia GG. catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. Bioinformatics. 2013;29:2928–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Ma S, Dong Z, Cui Q, Liu JY, Zhang JT. EIF3I regulation of protein synthesis, cell proliferation, cell cycle progression, and tumorigenesis. Cancer Lett. 2021;500:11–20.

    Article  CAS  PubMed  Google Scholar 

  28. Li Y, Xie P, Lu L, Wang J, Diao L, Liu Z, et al. An integrated bioinformatics platform for investigating the human E3 ubiquitin ligase-substrate interaction network. Nat Commun. 2017;8:347.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, et al. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics. 2011;10:M111.013284.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, et al. Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell. 2011;44:325–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Qin G, Tu X, Li H, Cao P, Chen X, Song J, et al. Long noncoding RNA p53-stabilizing and activating RNA promotes p53 signaling by inhibiting heterogeneous nuclear ribonucleoprotein K deSUMOylation and suppresses hepatocellular carcinoma. Hepatology. 2020;71:112–29.

    Article  CAS  PubMed  Google Scholar 

  32. Fu H, Liu N, Dong Q, Ma C, Yang J, Xiong J, et al. SENP6-mediated M18BP1 deSUMOylation regulates CENP-A centromeric localization. Cell Res. 2019;29:254–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Zhou L, Zheng L, Hu K, Wang X, Zhang R, Zou Y, et al. SUMOylation stabilizes hSSB1 and enhances the recruitment of NBS1 to DNA damage sites. Signal Transduct Target Ther. 2020;5:80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Aichem A, Sailer C, Ryu S, Catone N, Stankovic-Valentin N, Schmidtke G, et al. The ubiquitin-like modifier FAT10 interferes with SUMO activation. Nat Commun. 2019;10:4452.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Cui CP, Wong CC, Kai AK, Ho DW, Lau EY, Tsui YM, et al. SENP1 promotes hypoxia-induced cancer stemness by HIF-1α deSUMOylation and SENP1/HIF-1α positive feedback loop. Gut. 2017;66:2149–59.

    Article  CAS  PubMed  Google Scholar 

  36. Sun XX, Chen Y, Su Y, Wang X, Chauhan KM, Liang J, et al. SUMO protease SENP1 deSUMOylates and stabilizes c-Myc. Proc Natl Acad Sci USA. 2018;115:10983–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Qian X, Yang J, Qiu Q, Li X, Jiang C, Li J, et al. LCAT3, a novel m6A-regulated long non-coding RNA, plays an oncogenic role in lung cancer via binding with FUBP1 to activate c-MYC. J Hematol Oncol. 2021;14:112.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Jia Y, Duan Y, Liu T, Wang X, Lv W, Wang M, et al. LncRNA TTN-AS1 promotes migration, invasion, and epithelial mesenchymal transition of lung adenocarcinoma via sponging miR-142-5p to regulate CDK5. Cell Death Dis. 2019;10:573.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Wu Y, Yang X, Chen Z, Tian L, Jiang G, Chen F, et al. m6A-induced lncRNA RP11 triggers the dissemination of colorectal cancer cells via upregulation of Zeb1. Mol Cancer. 2019;18:87.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Xiao W, Zhang W, Huang H, Xie Y, Zhang Y, Guo X, et al. Cancer targeted gene therapy for inhibition of melanoma lung metastasis with EIF3I shRNA loaded liposomes. Mol Pharm. 2020;17:229–38.

    Article  CAS  PubMed  Google Scholar 

  41. Gong L, Millas S, Maul GG, Yeh ET. Differential regulation of sentrinized proteins by a novel sentrin-specific protease. J Biol Chem. 2000;275:3355–9.

    Article  CAS  PubMed  Google Scholar 

  42. Wei M, Huang X, Liao L, Tian Y, Zheng X. SENP1 decreases RNF168 phase separation to promote DNA damage repair and drug resistance in colon cancer. Cancer Res. 2023;83:2908–23.

    Article  CAS  PubMed  Google Scholar 

  43. Meyer KD, Jaffrey SR. The dynamic epitranscriptome: n6-methyladenosine and gene expression control. Nat Rev Mol Cell Biol. 2014;15:313–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Li J, Xie G, Tian Y, Li W, Wu Y, Chen F, et al. RNA m6A methylation regulates dissemination of cancer cells by modulating expression and membrane localization of β-catenin. Mol Ther. 2022;30:1578–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Zuo X, Chen Z, Gao W, Zhang Y, Wang J, Wang J, et al. M6A-mediated upregulation of LINC00958 increases lipogenesis and acts as a nanotherapeutic target in hepatocellular carcinoma. J Hematol Oncol. 2020;13:5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Jia G, Wang Y, Lin C, Lai S, Dai H, Wang Z, et al. LNCAROD enhances hepatocellular carcinoma malignancy by activating glycolysis through induction of pyruvate kinase isoform PKM2. J Exp Clin Cancer Res. 2021;40:299.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Han Y, Wang S, Zhang Z, Ma X, Li W, Zhang X, et al. In vivo imaging of protein-protein and RNA-protein interactions using novel far-red fluorescence complementation systems. Nucleic Acids Res. 2014;42:e103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Funding

This work as supported by the National Natural Science Foundation of China (No. 82002578), 1·3·5 project for disciplines of excellence–Clinical Research Incubation Project, West China Hospital, Sichuan University (No. 20HXFH021), 1.3.5 project for disciplines of excellence, West China Hospital, Sichuan University (No. ZYJC21049).

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J.L. and X.X. considered and designed the study. B.L., J.X., D.P. and G.N. performed experiments. B.L., X.X., N.W. and Y.W. did data analyses. J.L. and B.L. wrote the manuscript. J.L., B.L. and X. X contributed to the revision of manuscript. All authors read and approved the final manuscript.

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Correspondence to Jiong Lu.

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All animal experiments involved in this study were performed in conformity to the National Institutes of Health Guide for the Care and Use of Laboratory Animals following approval by the Laboratory Animal Ethnics Committees of West China Hospital of Sichuan University (approval number: 20220926005).

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Li, B., Xiong, X., Xu, J. et al. METTL3-mediated m6A modification of lncRNA TSPAN12 promotes metastasis of hepatocellular carcinoma through SENP1-depentent deSUMOylation of EIF3I. Oncogene 43, 1050–1062 (2024). https://doi.org/10.1038/s41388-024-02970-0

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