Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Copy number amplification and SP1-activated lncRNA MELTF-AS1 regulates tumorigenesis by driving phase separation of YBX1 to activate ANXA8 in non-small cell lung cancer

Oncogene volume 41, pages 3222–3238 (2022)Cite this article

Subjects

Abstract

Long non-coding RNAs (lncRNAs) are reported to play key roles in tumorigenesis. However, the mechanisms underlying lncRNA-mediated regulation of RNA-binding protein phase separation in tumorigenesis have not been completely elucidated. In this study, an oncogenic lncRNA MELTF-AS1 was identified using systematic data analysis, screening, and verification. MELTF-AS1 was markedly upregulated in non-small cell lung cancer (NSCLC). High MELTF-AS1 levels were associated with advanced tumor-node-metastasis stage (TNM), high tumor size, and decreased survival time. Functionally, MELTF-AS1 regulated cell proliferation and metastasis in vitro and in vivo. RNA sequencing analysis revealed that MELTF-AS1 knockdown specifically modulated genes associated with cell proliferation, apoptosis, and migration. Mechanistically, at the genome level, copy number amplification promoted MELTF-AS1 expression. At the transcriptional level, the transcription factor SP1 directly activated MELTF-AS1 transcription by binding to its promoter. Furthermore, MELTF-AS1 could directly bind and drive the phase separation of YBX1, which was an RNA-binding protein and involved in tumorigenesis, thus activating ANXA8 transcription and promoting tumorigenesis of NSCLC. Aberrant activation of ANXA8 and promotion of tumorigenesis have been found in a variety of tumors. These novel findings demonstrated the critical role of MELTF-AS1-driven phase separation-mediated transcriptional regulation and provided a potential novel diagnostic and therapeutic target for NSCLC.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Upregulated MELTF-AS1 expression levels in non-small cell lung carcinoma (NSCLC) tissues and their clinical significance.
Fig. 2: DNA copy number amplification and SP1 upregulate MELTF-AS1 expression in non-small cell lung carcinoma (NSCLC).
Fig. 3: Effects of MELTF-AS1 on non-small cell lung carcinoma (NSCLC) cell proliferation, migration, and invasion in vitro.
Fig. 4: Effects of MELTF-AS1 knockdown on tumor development and cell migration in vivo.
Fig. 5: MELTF-AS1 exerts its functions by interacting with YBX1.
Fig. 6: MELTF-AS1 regulated gene expression by directly promoting phase separation of YBX1 and condensate formation.
Fig. 7: Knockdown of MELTF-AS1 or YBX1 regulates the expression of genes involved in cell proliferation and metastasis.
Fig. 8: MELTF-AS1 regulates the expression of ANXA8 by interacting with YBX1.

Similar content being viewed by others

References

  1. Siegel RL, Miller KD, Fuchs HE, Jemal A. Cancer Statistics, 2021. CA Cancer J Clin. 2021;71:7–33.

    Article  PubMed  Google Scholar 

  2. Petrelli NJ, Winer EP, Brahmer J, Dubey S, Smith S, Thomas C, et al. Clinical Cancer Advances 2009: major research advances in cancer treatment, prevention, and screening−a report from the American Society of Clinical Oncology. J Clin Oncol. 2009;27:6052–69.

    Article  PubMed  Google Scholar 

  3. Camps C, del Pozo N, Blasco A, Blasco P, Sirera R. Importance of quality of life in patients with non-small-cell lung cancer. Clin Lung Cancer. 2009;10:83–90.

    Article  CAS  PubMed  Google Scholar 

  4. Esteller M. Non-coding RNAs in human disease. Nat Rev Genet. 2011;12:861–74.

    Article  CAS  PubMed  Google Scholar 

  5. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, et al. Landscape of transcription in human cells. Nature. 2012;489:101–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Prensner JR, Chinnaiyan AM. The emergence of lncRNAs in cancer biology. Cancer Disco. 2011;1:391–407.

    Article  CAS  Google Scholar 

  7. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10:155–9.

    Article  CAS  PubMed  Google Scholar 

  8. Gutschner T, Hammerle M, Eissmann M, Hsu J, Kim Y, Hung G, et al. The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res. 2013;73:1180–9.

    Article  CAS  PubMed  Google Scholar 

  9. Chen Z, Li JL, Lin S, Cao C, Gimbrone NT, Yang R, et al. cAMP/CREB-regulated LINC00473 marks LKB1-inactivated lung cancer and mediates tumor growth. J Clin Invest. 2016;126:2267–79.

    Article  PubMed  PubMed Central  Google Scholar 

  10. Zhang E, Han L, Yin D, He X, Hong L, Si X, et al. H3K27 acetylation activated-long non-coding RNA CCAT1 affects cell proliferation and migration by regulating SPRY4 and HOXB13 expression in esophageal squamous cell carcinoma. Nucleic Acids Res. 2017;45:3086–101.

    Article  CAS  PubMed  Google Scholar 

  11. Yin D, Lu X, Su J, He X, De W, Yang J, et al. Long noncoding RNA AFAP1-AS1 predicts a poor prognosis and regulates non-small cell lung cancer cell proliferation by epigenetically repressing p21 expression. Mol Cancer. 2018;17:92.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  12. Zhang E, He X, Zhang C, Su J, Lu X, Si X, et al. A novel long noncoding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding to YBX1. Genome Biol. 2018;19:154.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  13. Liu X, Lu X, Zhen F, Jin S, Yu T, Zhu Q, et al. LINC00665 induces acquired resistance to gefitinib through recruiting EZH2 and activating PI3K/AKT pathway in NSCLC. Mol Ther Nucleic Acids. 2019;16:155–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Sabari BR, Dall'Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K. et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018;361: eaar3958.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Banani SF, Lee HO, Hyman AA, Rosen MK. Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol. 2017;18:285–98.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Jiang S, Fagman JB, Chen C, Alberti S, Liu B. Protein phase separation and its role in tumorigenesis. Elife. 2020;9: e60264.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Alberti S, Dormann D. Liquid-liquid phase separation in disease. Annu Rev Genet. 2019;53:171–94.

    Article  CAS  PubMed  Google Scholar 

  18. Lin C, Yang L. Long noncoding RNA in cancer: wiring signaling circuitry. Trends Cell Biol. 2018;28:287–301.

    Article  CAS  PubMed  Google Scholar 

  19. Schimke RT. The search for early genetic events in tumorigenesis: an amplification paradigm. Cancer Cells. 1990;2:149–51.

    CAS  PubMed  Google Scholar 

  20. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, et al. The landscape of somatic copy-number alteration across human cancers. Nature. 2010;463:899–905.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Lin M, Smith LT, Smiraglia DJ, Kazhiyur-Mannar R, Lang JC, Schuller DE, et al. DNA copy number gains in head and neck squamous cell carcinoma. Oncogene. 2006;25:1424–33.

    Article  CAS  PubMed  Google Scholar 

  22. La-Touche S, Lemetre C, Lambros M, Stankiewicz E, Ng CK, Weigelt B, et al. DNA copy number aberrations, and human papillomavirus status in penile carcinoma. Clinico-pathological correlations and potential driver genes. PLoS ONE. 2016;11:e0146740.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Ricciotti RW, Baraff AJ, Jour G, Kyriss M, Wu Y, Liu Y, et al. High amplification levels of MDM2 and CDK4 correlate with poor outcome in patients with dedifferentiated liposarcoma: a cytogenomic microarray analysis of 47 cases. Cancer Genet. 2017;218-219:69–80.

    Article  CAS  PubMed  Google Scholar 

  24. Li L, Davie JR. The role of Sp1 and Sp3 in normal and cancer cell biology. Ann Anat. 2010;192:275–83.

    Article  CAS  PubMed  Google Scholar 

  25. Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45:W98–W102.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Yu XX, Murray SF, Pandey SK, Booten SL, Bao D, Song XZ, et al. Antisense oligonucleotide reduction of DGAT2 expression improves hepatic steatosis and hyperlipidemia in obese mice. Hepatology. 2005;42:362–71.

    Article  CAS  PubMed  Google Scholar 

  27. Yang F, Wei J, Zhang S, Zhang X. Shrimp miR-S8 suppresses the stemness of human melanoma stem-like cells by targeting the transcription factor YB-1. Cancer Res. 2017;77:5543–53.

    Article  CAS  PubMed  Google Scholar 

  28. Kosnopfel C, Sinnberg T, Schittek B. Y-box binding protein 1−a prognostic marker and target in tumour therapy. Eur J Cell Biol. 2014;93:61–70.

    Article  CAS  PubMed  Google Scholar 

  29. Goodarzi H, Liu X, Nguyen HC, Zhang S, Fish L, Tavazoie SF. Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell. 2015;161:790–802.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Shibahara K, Sugio K, Osaki T, Uchiumi T, Maehara Y, Kohno K, et al. Nuclear expression of the Y-box binding protein, YB-1, as a novel marker of disease progression in non-small cell lung cancer. Clin Cancer Res. 2001;7:3151–5.

    CAS  PubMed  Google Scholar 

  31. Evdokimova V, Tognon C, Ng T, Ruzanov P, Melnyk N, Fink D, et al. Translational activation of snail1 and other developmentally regulated transcription factors by YB-1 promotes an epithelial-mesenchymal transition. Cancer Cell. 2009;15:402–15.

    Article  CAS  PubMed  Google Scholar 

  32. Li D, Liu X, Zhou J, Hu J, Zhang D, Liu J, et al. Long noncoding RNA HULC modulates the phosphorylation of YB-1 through serving as a scaffold of extracellular signal-regulated kinase and YB-1 to enhance hepatocarcinogenesis. Hepatology. 2017;65:1612–27.

    Article  CAS  PubMed  Google Scholar 

  33. Deng SJ, Chen HY, Ye Z, Deng SC, Zhu S, Zeng Z, et al. Hypoxia-induced LncRNA-BX111 promotes metastasis and progression of pancreatic cancer through regulating ZEB1 transcription. Oncogene. 2018;37:5811–28.

    Article  CAS  PubMed  Google Scholar 

  34. Imada K, Shiota M, Kohashi K, Kuroiwa K, Song Y, Sugimoto M, et al. Mutual regulation between Raf/MEK/ERK signaling and Y-box-binding protein-1 promotes prostate cancer progression. Clin Cancer Res. 2013;19:4638–50.

    Article  CAS  PubMed  Google Scholar 

  35. Roden C, Gladfelter AS. RNA contributions to the form and function of biomolecular condensates. Nat Rev Mol Cell Biol. 2021;22:183–95.

    Article  CAS  PubMed  Google Scholar 

  36. Wu M, Xu G, Han C, Luan PF, Xing YH, Nan F, et al. lncRNA SLERT controls phase separation of FC/DFCs to facilitate Pol I transcription. Science. 2021;373:547–55.

    Article  CAS  PubMed  Google Scholar 

  37. Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell. 2013;154:26–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Stein T, Price KN, Morris JS, Heath VJ, Ferrier RK, Bell AK, et al. Annexin A8 is up-regulated during mouse mammary gland involution and predicts poor survival in breast cancer. Clin Cancer Res. 2005;11:6872–9.

    Article  CAS  PubMed  Google Scholar 

  39. Hata H, Tatemichi M, Nakadate T. Involvement of annexin A8 in the properties of pancreatic cancer. Mol Carcinog. 2014;53:181–91.

    Article  CAS  PubMed  Google Scholar 

  40. Sarkar A, Yang P, Fan YH, Mu ZM, Hauptmann R, Adolf GR, et al. Regulation of the expression of annexin VIII in acute promyelocytic leukemia. Blood. 1994;84:279–86.

    Article  CAS  PubMed  Google Scholar 

  41. Li C, Tan F, Pei Q, Zhou Z, Zhou Y, Zhang L, et al. Non-coding RNA MFI2-AS1 promotes colorectal cancer cell proliferation, migration and invasion through miR-574-5p/MYCBP axis. Cell Prolif. 2019;52:e12632.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Flippot R, Mouawad R, Spano JP, Roupret M, Comperat E, Bitker MO, et al. Expression of long non-coding RNA MFI2-AS1 is a strong predictor of recurrence in sporadic localized clear-cell renal cell carcinoma. Sci Rep. 2017;7:8540.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Wei Y, Wang Z, Zong Y, Deng D, Chen P, Lu J. LncRNA MFI2-AS1 promotes HCC progression and metastasis by acting as a competing endogenous RNA of miR-134 to upregulate FOXM1 expression. Biomed Pharmacother. 2020;125:109890.

    Article  CAS  PubMed  Google Scholar 

  44. Liu K, Liu J, Bo QF. MFI2-AS1 regulates the aggressive phenotypes in glioma by modulating MMP14 via a positive feedback loop. Eur Rev Med Pharm Sci. 2019;23:5884–95.

    CAS  Google Scholar 

  45. Tseng YY, Moriarity BS, Gong W, Akiyama R, Tiwari A, Kawakami H, et al. PVT1 dependence in cancer with MYC copy-number increase. Nature. 2014;512:82–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Wierstra I. Sp1: emerging roles−beyond constitutive activation of TATA-less housekeeping genes. Biochem Biophys Res Commun. 2008;372:1–13.

    Article  CAS  PubMed  Google Scholar 

  47. Jungert K, Buck A, von Wichert G, Adler G, Konig A, Buchholz M, et al. Sp1 is required for transforming growth factor-beta-induced mesenchymal transition and migration in pancreatic cancer cells. Cancer Res. 2007;67:1563–70.

    Article  CAS  PubMed  Google Scholar 

  48. Batista PJ, Chang HY. Long noncoding RNAs: cellular address codes in development and disease. Cell. 2013;152:1298–307.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Liu Y, Zhao J, Zhang W, Gan J, Hu C, Huang G, et al. lncRNA GAS5 enhances G1 cell cycle arrest via binding to YBX1 to regulate p21 expression in stomach cancer. Sci Rep. 2015;5:10159.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Boija A, Klein IA, Young RA. Biomolecular condensates and cancer. Cancer Cell. 2021;39:174–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Boija A, Klein IA, Sabari BR, Dall’Agnese A, Coffey EL, Zamudio AV, et al. Transcription factors activate genes through the phase-separation capacity of their activation domains. Cell. 2018;175:1842–55.

    Article  CAS  PubMed  Google Scholar 

  52. Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, et al. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature. 2018;561:132–6.

    Article  CAS  PubMed  Google Scholar 

  53. Yan X, Yin J, Yao H, Mao N, Yang Y, Pan L. Increased expression of annexin A3 is a mechanism of platinum resistance in ovarian cancer. Cancer Res. 2010;70:1616–24.

    Article  CAS  PubMed  Google Scholar 

  54. Song J, Shih IeM, Salani R, Chan DW, Zhang Z. Annexin XI is associated with cisplatin resistance and related to tumor recurrence in ovarian cancer patients. Clin Cancer Res. 2007;13:6842–9.

    Article  CAS  PubMed  Google Scholar 

  55. Li J, Han L, Roebuck P, Diao L, Liu L, Yuan Y, et al. TANRIC: an interactive open platform to explore the function of lncRNAs in cancer. Cancer Res. 2015;75:3728–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors thank NovelBioinformatics Ltd., Co. for the support of bioinformatics analysis with their NovelBrain Cloud Analysis Platform (www.novelbrain.com).

Funding

This work was supported by the National Natural Science Foundation of China [82172992, 81972188 and 82103133], Natural Science Foundation of Jiangsu Province [BK20211253 and BK20210973], China Postdoctoral Science Foundation (2020M671395), the Medical Important Talents [ZDRCA2016024], the Program for Innovative Research Team of Nanjing Medical University [JX102GSP201727], and the Wu Jie-ping Foundation [320.6799.15032].

Author information

Author notes

  1. These authors contributed equally: Xiyi Lu, Jing Wang, Wei Wang, Chenfei Lu.

Authors and Affiliations

  1. Department of Oncology, The first Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China

    Xiyi Lu, Tianyu Qu, Xinyin Liu & Renhua Guo

  2. Department of Anatomy, Histology and Embryology, State Key Laboratory of Reproductive Medicine, The Research Center for Bone and Stem Cells, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China

    Jing Wang & Xuezhi He

  3. Department of Thoracic surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China

    Wei Wang

  4. Department of Clinical Medicine, Medical College of Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China

    Chenfei Lu

  5. Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China

    Erbao Zhang

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

    Erbao Zhang

Authors
  1. Xiyi Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jing Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chenfei Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tianyu Qu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xuezhi He
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xinyin Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Renhua Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Erbao Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

EZ and RG conceived the project and designed the experiments. XL, JW and CL started and performed majority of the experiments. WW, TQ and XL collected the NSCLC samples. XH provided technical and administrative support. XL analyzed results and wrote the manuscript. RG and EZ contributed to manuscript revision and supervised all experiments. All authors read and provided suggestions during manuscript preparation.

Corresponding authors

Correspondence to Renhua Guo or Erbao Zhang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lu, X., Wang, J., Wang, W. et al. Copy number amplification and SP1-activated lncRNA MELTF-AS1 regulates tumorigenesis by driving phase separation of YBX1 to activate ANXA8 in non-small cell lung cancer. Oncogene 41, 3222–3238 (2022). https://doi.org/10.1038/s41388-022-02292-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41388-022-02292-z

This article is cited by

Search

Advanced search

Quick links