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.

Long noncoding RNA MALAT1 suppresses breast cancer metastasis

Abstract

MALAT1 has previously been described as a metastasis-promoting long noncoding RNA (lncRNA). We show here, however, that targeted inactivation of the Malat1 gene in a transgenic mouse model of breast cancer, without altering the expression of its adjacent genes, promotes lung metastasis, and that this phenotype can be reversed by genetic add-back of Malat1. Similarly, knockout of MALAT1 in human breast cancer cells induces their metastatic ability, which is reversed by re-expression of Malat1. Conversely, overexpression of Malat1 suppresses breast cancer metastasis in transgenic, xenograft, and syngeneic models. Mechanistically, the MALAT1 lncRNA binds and inactivates the prometastatic transcription factor TEAD, preventing TEAD from associating with its co-activator YAP and target gene promoters. Moreover, MALAT1 levels inversely correlate with breast cancer progression and metastatic ability. These findings demonstrate that MALAT1 is a metastasis-suppressing lncRNA rather than a metastasis promoter in breast cancer, calling for rectification of the model for this highly abundant and conserved lncRNA.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Targeted inactivation and restoration of Malat1 in mice suggest that Malat1 is a suppressor of breast cancer lung metastasis.
Fig. 2: Targeted transgenic overexpression of Malat1 in mice inhibits breast cancer metastasis.
Fig. 3: Malat1 inhibits the metastatic ability of breast cancer cells.
Fig. 4: MALAT1 interacts with TEAD-family members.
Fig. 5: MALAT1 inactivates TEAD.
Fig. 6: ITGB4 and VEGFA are TEAD target genes and are regulated by MALAT1.

Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request. The RNA-seq data have been deposited at the Gene Expression Omnibus under accession number GSE110239.

References

  1. 1.

    Evans, J. R., Feng, F. Y. & Chinnaiyan, A. M. The bright side of dark matter: lncRNAs in cancer. J. Clin. Invest. 126, 2775–2782 (2016).

    Article  Google Scholar 

  2. 2.

    Zhang, B. et al. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep. 2, 111–123 (2012).

    CAS  Article  Google Scholar 

  3. 3.

    Wilusz, J. E., Freier, S. M. & Spector, D. L. 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135, 919–932 (2008).

    CAS  Article  Google Scholar 

  4. 4.

    Hutchinson, J. N. et al. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8, 39 (2007).

    Article  Google Scholar 

  5. 5.

    Tripathi, V. et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 39, 925–938 (2010).

    CAS  Article  Google Scholar 

  6. 6.

    Eissmann, M. et al. Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol. 9, 1076–1087 (2012).

    CAS  Article  Google Scholar 

  7. 7.

    Nakagawa, S. et al. Malat1 is not an essential component of nuclear speckles in mice. RNA 18, 1487–1499 (2012).

    CAS  Article  Google Scholar 

  8. 8.

    Li, L. et al. Role of human noncoding RNAs in the control of tumorigenesis. Proc. Natl Acad. Sci. USA 106, 12956–12961 (2009).

    CAS  Article  Google Scholar 

  9. 9.

    Ji, Q. et al. Long non-coding RNA MALAT1 promotes tumour growth and metastasis in colorectal cancer through binding to SFPQ and releasing oncogene PTBP2 from SFPQ/PTBP2 complex. Br. J. Cancer 111, 736–748 (2014).

    CAS  Article  Google Scholar 

  10. 10.

    Cao, S. et al. Tumor-suppressive function of long noncoding RNA MALAT1 in glioma cells by suppressing miR-155 expression and activating FBXW7 function. Am. J. Cancer Res. 6, 2561–2574 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11.

    Han, Y. et al. Tumor-suppressive function of long noncoding RNA MALAT1 in glioma cells by downregulation of MMP2 and inactivation of ERK/MAPK signaling. Cell Death Dis. 7, e2123 (2016).

    CAS  Article  Google Scholar 

  12. 12.

    Latorre, E. et al. The ribonucleic complex HuR-MALAT1 represses CD133 expression and suppresses epithelial-mesenchymal transition in breast cancer. Cancer Res. 76, 2626–2636 (2016).

    CAS  Article  Google Scholar 

  13. 13.

    Guy, C. T., Cardiff, R. D. & Muller, W. J. Induction of mammary tumors by expression of polyomavirus middle T oncogene: a transgenic mouse model for metastatic disease. Mol. Cell. Biol. 12, 954–961 (1992).

    CAS  Article  Google Scholar 

  14. 14.

    Arun, G. et al. Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. Genes Dev. 30, 34–51 (2016).

    CAS  Article  Google Scholar 

  15. 15.

    Bassett, A. R. et al. Considerations when investigating lncRNA function in vivo. eLife 3, e03058 (2014).

    Article  Google Scholar 

  16. 16.

    Yin, Y. et al. Opposing roles for the lncRNA Haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation. Cell Stem Cell 16, 504–516 (2015).

    CAS  Article  Google Scholar 

  17. 17.

    Gutschner, T. et al. The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res. 73, 1180–1189 (2013).

    CAS  Article  Google Scholar 

  18. 18.

    Jadaliha, M. et al. Functional and prognostic significance of long non-coding RNA MALAT1 as a metastasis driver in ER negative lymph node negative breast cancer. Oncotarget 7, 40418–40436 (2016).

    Article  Google Scholar 

  19. 19.

    Lin, A., Giuliano, C. J., Sayles, N. M. & Sheltzer, J. M. CRISPR/Cas9 mutagenesis invalidates a putative cancer dependency targeted in on-going clinical trials. eLife 6, e24179 (2017).

    Article  Google Scholar 

  20. 20.

    Huang, H. T. et al. MELK is not necessary for the proliferation of basal-like breast cancer cells. eLife 6, e26693 (2017).

    Article  Google Scholar 

  21. 21.

    Lin, E. Y. et al. Progression to malignancy in the polyoma middle T oncoprotein mouse breast cancer model provides a reliable model for human diseases. Am. J. Pathol. 163, 2113–2126 (2003).

    Article  Google Scholar 

  22. 22.

    Davie, S. A. et al. Effects of FVB/NJ and C57Bl/6J strain backgrounds on mammary tumor phenotype in inducible nitric oxide synthase deficient mice. Transgenic. Res. 16, 193–201 (2007).

    CAS  Article  Google Scholar 

  23. 23.

    Kim, J. et al. Ablation of miR-10b suppresses oncogene-induced mammary tumorigenesis and metastasis and reactivates tumor-suppressive pathways. Cancer Res. 76, 6424–6435 (2016).

    CAS  Article  Google Scholar 

  24. 24.

    Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012).

    CAS  Article  Google Scholar 

  25. 25.

    Minn, A. J. et al. Genes that mediate breast cancer metastasis to lung. Nature 436, 518–524 (2005).

    CAS  Article  Google Scholar 

  26. 26.

    Aparicio-Prat, E. et al. DECKO: single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs. BMC Genomics 16, 846 (2015).

    Article  Google Scholar 

  27. 27.

    The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012).

    Article  Google Scholar 

  28. 28.

    Gyorffy, B. et al. An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients. Breast Cancer Res. Treat. 123, 725–731 (2010).

    Article  Google Scholar 

  29. 29.

    Aslakson, C. J. & Miller, F. R. Selective events in the metastatic process defined by analysis of the sequential dissemination of subpopulations of a mouse mammary tumor. Cancer Res. 52, 1399–1405 (1992).

    CAS  PubMed  Google Scholar 

  30. 30.

    Chu, C. et al. Systematic discovery of Xist RNA binding proteins. Cell 161, 404–416 (2015).

    CAS  Article  Google Scholar 

  31. 31.

    Yoon, J. H. et al. Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination. Nat. Commun. 4, 2939 (2013).

    Article  Google Scholar 

  32. 32.

    Yoon, J. H. & Gorospe, M. Cross-linking immunoprecipitation and qPCR (CLIP-qPCR) analysis to map interactions between long noncoding RNAs and RNA-binding proteins. Methods Mol. Biol. 1402, 11–17 (2016).

    CAS  Article  Google Scholar 

  33. 33.

    Li, Z. et al. Structural insights into the YAP and TEAD complex. Genes Dev. 24, 235–240 (2010).

    CAS  Article  Google Scholar 

  34. 34.

    Pobbati, A. V. & Hong, W. Emerging roles of TEAD transcription factors and its coactivators in cancers. Cancer Biol. Ther. 14, 390–398 (2013).

    CAS  Article  Google Scholar 

  35. 35.

    Pan, D. The hippo signaling pathway in development and cancer. Dev. Cell. 19, 491–505 (2010).

    CAS  Article  Google Scholar 

  36. 36.

    Zhao, B., Li, L., Lei, Q. & Guan, K. L. The Hippo-YAP pathway in organ size control and tumorigenesis: an updated version. Genes Dev. 24, 862–874 (2010).

    CAS  Article  Google Scholar 

  37. 37.

    Moroishi, T., Hansen, C. G. & Guan, K. L. The emerging roles of YAP and TAZ in cancer. Nat. Rev. Cancer 15, 73–79 (2015).

    CAS  Article  Google Scholar 

  38. 38.

    Zanconato, F. et al. Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth. Nat. Cell Biol. 17, 1218–1227 (2015).

    CAS  Article  Google Scholar 

  39. 39.

    Dupont, S. et al. Role of YAP/TAZ in mechanotransduction. Nature 474, 179–183 (2011).

    CAS  Article  Google Scholar 

  40. 40.

    Stein, C. et al. YAP1 exerts its transcriptional control via TEAD-mediated activation of enhancers. PLoS Genet. 11, e1005465 (2015).

    Article  Google Scholar 

  41. 41.

    Zhao, B. et al. TEAD mediates YAP-dependent gene induction and growth control. Genes Dev. 22, 1962–1971 (2008).

    CAS  Article  Google Scholar 

  42. 42.

    Lian, I. et al. The role of YAP transcription coactivator in regulating stem cell self-renewal and differentiation. Genes Dev. 24, 1106–1118 (2010).

    CAS  Article  Google Scholar 

  43. 43.

    Hoshino, A. et al. Tumour exosome integrins determine organotropic metastasis. Nature 527, 329–335 (2015).

    CAS  Article  Google Scholar 

  44. 44.

    Chao, C., Lotz, M. M., Clarke, A. C. & Mercurio, A. M. A function for the integrin alpha6beta4 in the invasive properties of colorectal carcinoma cells. Cancer Res. 56, 4811–4819 (1996).

    CAS  PubMed  Google Scholar 

  45. 45.

    Guo, W. et al. β4 integrin amplifies ErbB2 signaling to promote mammary tumorigenesis. Cell 126, 489–502 (2006).

    CAS  Article  Google Scholar 

  46. 46.

    Leng, C. et al. An integrin beta4-EGFR unit promotes hepatocellular carcinoma lung metastases by enhancing anchorage independence through activation of FAK-AKT pathway. Cancer Lett. 376, 188–196 (2016).

    CAS  Article  Google Scholar 

  47. 47.

    Goel, H. L. & Mercurio, A. M. VEGF targets the tumour cell. Nat. Rev. Cancer 13, 871–882 (2013).

    CAS  Article  Google Scholar 

  48. 48.

    Takaoka, A. S. et al. Cloning and characterization of the human β4-integrin gene promoter and enhancers. J. Biol. Chem. 273, 33848–33855 (1998).

    CAS  Article  Google Scholar 

  49. 49.

    Wood, L. W. et al. Thyroid transcription factor 1 reprograms angiogenic activities of secretome. Sci. Rep. 6, 19857 (2016).

    CAS  Article  Google Scholar 

  50. 50.

    Leung, D. W., Cachianes, G., Kuang, W. J., Goeddel, D. V. & Ferrara, N. Vascular endothelial growth factor is a secreted angiogenic mitogen. Science 246, 1306–1309 (1989).

    CAS  Article  Google Scholar 

  51. 51.

    Bhattacharya, R. et al. Intracrine VEGF signalling mediates colorectal cancer cell migration and invasion. Br. J. Cancer 117, 848–855 (2017).

    CAS  Article  Google Scholar 

  52. 52.

    Luo, M. et al. VEGF/NRP-1axis promotes progression of breast cancer via enhancement of epithelial-mesenchymal transition and activation of NF-κB and β-catenin. Cancer Lett. 373, 1–11 (2016).

    CAS  Article  Google Scholar 

  53. 53.

    Oommen, S., Gupta, S. K. & Vlahakis, N. E. Vascular endothelial growth factor A (VEGF-A) induces endothelial and cancer cell migration through direct binding to integrin α9β1: identification of a specific α9β1 binding site. J. Biol. Chem. 286, 1083–1092 (2011).

    CAS  Article  Google Scholar 

  54. 54.

    Perrot-Applanat, M. & Di Benedetto, M. Autocrine functions of VEGF in breast tumor cells: adhesion, survival, migration and invasion. Cell Adh. Migr. 6, 547–553 (2012).

    Article  Google Scholar 

  55. 55.

    Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014).

    CAS  Article  Google Scholar 

  56. 56.

    Stewart, S. A. et al. Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA 9, 493–501 (2003).

    CAS  Article  Google Scholar 

  57. 57.

    Chu, C., Quinn, J. & Chang, H. Y. Chromatin isolation by RNA purification (ChIRP). J. Vis. Exp. 61, e3912 (2012).

    Google Scholar 

  58. 58.

    Vogt, M. & Taylor, V. Cross-linked RNA immunoprecipitation.Bio. Protoc. 3, e398 (2013).

    Article  Google Scholar 

  59. 59.

    Neve, R. M. et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 10, 515–527 (2006).

    CAS  Article  Google Scholar 

  60. 60.

    Dai, X., Cheng, H., Bai, Z. & Li, J. Breast cancer cell line classification and its relevance with breast tumor subtyping. J. Cancer 8, 3131–3141 (2017).

    Article  Google Scholar 

  61. 61.

    Jiang, G. et al. Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancer. BMC Genomics 17(Suppl 7), 525 (2016).

    Article  Google Scholar 

Download references

Acknowledgements

We thank W. Muller for providing MMTV-PyMT mice (C57BL/6 background), X. Zhang for providing luciferase-expressing LM2 cells, and J. Jacobson and L. Xin for providing ITGB4–luciferase and FU-luciferase-CRW/RFP constructs, respectively. We thank J. Zhang and MD Anderson’s shRNA and ORFeome Core, Small Animal Imaging Facility, Flow Cytometry and Cellular Imaging Core Facility, Sequencing and Microarray Facility, and Characterized Cell Line Core Facility for technical assistance. We thank all members of the Ma laboratory for discussions; J. Chen for critical reading of the manuscript; and J.-H. Yoon and M. Gorospe for advice on the CLIP assay. L.M. is supported by US National Institutes of Health (NIH) grants R01CA166051 and R01CA181029; a Cancer Prevention and Research Institute of Texas (CPRIT) grant (RP150319); and a Stand Up To Cancer Innovative Research Grant (403235). M.J.Y. was supported in part by NIH grants R01CA164346 and R01CA200703, and CPRIT RP140402. M.-C.H. is supported by National Breast Cancer Foundation Inc. and The University of Texas MD Anderson-China Medical University and Hospital Sister Institution Fund. H. Liang is supported by NIH grants R01CA175486 and U24CA209851. M.J.E is supported by CPRIT grant RR140033. B.G. is supported by NIH grants R01CA181196 and R01CA190370.

Author information

Affiliations

Authors

Contributions

J.K., Y.S. and L.M. conceived and designed the study. J.K. performed most experiments. H.-L.P. cloned mouse Malat1. B.-J.K. and M.J.E. performed mass-spectrometric analysis. F.Y. and Z.X. generated some constructs and cell lines and performed some experiments. Z.H. and M.-C.H. assisted with microscopy. Y.W. and H. Liang performed RNA-seq and other computational data analyses. A.N.S., S.E.L. and B.N.T. maintained and managed mouse colonies. H. Lee, Z.Z. and B.G. provided reagents and technical assistance. S.N. provided Malat1-knockout mice. M.J.Y. performed histopathological analysis. Y.S. generated some constructs and provided substantial intellectual input. J.K. and L.M. wrote the manuscript with input from all other authors. L.M. provided scientific direction, established collaborations, and allocated funding for this study.

Corresponding author

Correspondence to Li Ma.

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

Supplementary Text and Figures

Supplementary Figures 1–10, Supplementary Tables 1–3 and Supplementary Note

Reporting Summary

Supplementary Video 1

Time-lapse video microscopy of control MDA-MB-231 cells

Supplementary Video 2

Time-lapse video microscopy of MALAT1-knockout MDA-MB-231 cells

Supplementary Video 3

Time-lapse video microscopy of MALAT1-knockout MDA-MB-231 cells with ectopic expression of mouse Malat1

Supplementary Video 4

Time-lapse video microscopy of control LM2 cells

Supplementary Video 5

Time-lapse video microscopy of Malat1-overexpressing LM2 cells

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Kim, J., Piao, HL., Kim, BJ. et al. Long noncoding RNA MALAT1 suppresses breast cancer metastasis. Nat Genet 50, 1705–1715 (2018). https://doi.org/10.1038/s41588-018-0252-3

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing