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Histone H3K9 methyltransferase SETDB1 augments invadopodia formation to promote tumor metastasis

Oncogene volume 41, pages 3370–3380 (2022)Cite this article

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Abstract

Non-small cell lung cancer (NSCLC) is one of leading causes of cancer-related mortality worldwide, which harbors various accumulated genetic and epigenetic abnormalities. Histone methyltransferase SETDB1 is a pivotal epigenetic regulator whose focal amplification and upregulation are commonly detected in NSCLC. However, molecular mechanisms underlying the pro-oncogenic function of SETDB1 remain poorly characterized. Here, we demonstrate that SETDB1 augments the migration and invasion capabilities of NSCLC cells by reinforcing invadopodia formation and mediated ECM degradation. At the molecular level, SETDB1 suppresses the expression of FOXA2, a crucial tumor and metastasis suppressor via coordinated epigenetic mechanisms – SETDB1 not only catalyzes histone H3K9 methylation on FOXA2 genomic locus, but also recruits DNMT3A to regulate DNA methylation on CpG island. Consequently, depletion of Setdb1 in murine lung adenocarcinoma cells completely abolished their full and spontaneous metastatic capabilities in mouse xenograft models. These findings together establish the pro-metastasis activity of SETDB1 in NSCLC and elucidate the underlying cellular and molecular mechanisms.

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Fig. 1: SETDB1 promotes NSCLC cell migration and invasion.
Fig. 2: SETDB1 promotes invadopodia formation and ECM degradation.
Fig. 3: SETDB1 represses FOXA2 to promote migration and invasion of NSCLC cells.
Fig. 4: SETDB1 cooperates with DNMT3A and DNA methylation for FOXA2 silencing.
Fig. 5: Setdb1 represses Foxa2 expression and promotes motility and invasiveness of murine KrasG12D/+; p53fl/fl lung adenocarcinoma cells.
Fig. 6: SETDB1 promotes NSCLC malignant progression and metastasis.

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Data availability

The datasets generated and analyzed during the current study are available from the corresponding author on reasonable request.

References

  1. Siegel RL, Miller KD, Jemal A. Cancer statistics, 2017. CA Cancer J Clin. 2017;67:7–30.

    Article  PubMed  Google Scholar 

  2. Lee T, Lee B, Choi YL, Han J, Ahn MJ, Um SW. Non-small cell lung cancer with concomitant EGFR, KRAS, and ALK mutation: clinicopathologic features of 12 cases. J Pathol Transl Med. 2016;50:197–203.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Duruisseaux M, Esteller M. Lung cancer epigenetics: From knowledge to applications. Semin Cancer Biol. 2018;51:116–28.

    Article  CAS  PubMed  Google Scholar 

  4. Mozzetta C, Boyarchuk E, Pontis J, Ait-Si-Ali S. Sound of silence: the properties and functions of repressive Lys methyltransferases. Nat Rev Mol Cell Biol. 2015;16:499–513.

    Article  CAS  PubMed  Google Scholar 

  5. Dodge JE, Kang YK, Beppu H, Lei H, Li E. Histone H3-K9 methyltransferase ESET is essential for early development. Mol Cell Biol. 2004;24:2478–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Fukuda K, Shinkai Y. SETDB1-mediated silencing of retroelements. Viruses. 2020;12:596–612.

    Article  CAS  PubMed Central  Google Scholar 

  7. Gauchier M, Kan S, Barral A, Sauzet S, Agirre E, Bonnell E, et al. SETDB1-dependent heterochromatin stimulates alternative lengthening of telomeres. Sci Adv. 2019;5:eaav3673.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Yuan P, Han J, Guo G, Orlov YL, Huss M, Loh YH, et al. Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev. 2009;23:2507–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Juznic L, Peuker K, Strigli A, Brosch M, Herrmann A, Hasler R, et al. SETDB1 is required for intestinal epithelial differentiation and the prevention of intestinal inflammation. Gut. 2021;70:485–98.

    Article  CAS  PubMed  Google Scholar 

  10. Takikita S, Muro R, Takai T, Otsubo T, Kawamura YI, Dohi T, et al. A histone methyltransferase ESET is critical for T cell development. J Immunol. 2016;197:2269–79.

    Article  CAS  PubMed  Google Scholar 

  11. Ceol CJ, Houvras Y, Jane-Valbuena J, Bilodeau S, Orlando DA, Battisti V, et al. The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. Nature. 2011;471:513–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Rodriguez-Paredes M, Martinez de Paz A, Simo-Riudalbas L, Sayols S, Moutinho C, Moran S, et al. Gene amplification of the histone methyltransferase SETDB1 contributes to human lung tumorigenesis. Oncogene. 2014;33:2807–13.

    Article  CAS  PubMed  Google Scholar 

  13. Cruz-Tapias P, Zakharova V, Perez-Fernandez OM, Mantilla W, Ram I-CS, Ait-Si-Ali S. Expression of the major and pro-oncogenic H3K9 lysine methyltransferase SETDB1 in non-small cell lung cancer. Cancers. 2019;11:1134–53.

  14. Kang YK, Min B. SETDB1 overexpression sets an intertumoral transcriptomic divergence in non-small cell lung carcinoma. Front Genet. 2020;11:573515.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Strepkos D, Markouli M, Klonou A, Papavassiliou AG, Piperi C. Histone methyltransferase SETDB1: a common denominator of tumorigenesis with therapeutic potential. Cancer Res. 2021;81:525–34.

    Article  CAS  PubMed  Google Scholar 

  16. Zhang SM, Cai WL, Liu X, Thakral D, Luo J, Chan LH, et al. KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements. Nature. 2021;598:682–7.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Griffin GK, Wu J, Iracheta-Vellve A, Patti JC, Hsu J, Davis T, et al. Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. Nature. 2021;595:309–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Guler GD, Tindell CA, Pitti R, Wilson C, Nichols K, KaiWai Cheung T, et al. Repression of stress-induced LINE-1 expression protects cancer cell subpopulations from lethal drug exposure. Cancer Cell. 2017;32:221–37.e13.

    Article  CAS  PubMed  Google Scholar 

  19. Lafuente-Sanchis A, Zuniga A, Galbis JM, Cremades A, Estors M, Martinez-Hernandez NJ, et al. Prognostic value of ERCC1, RRM1, BRCA1 and SETDB1 in early stage of non-small cell lung cancer. Clin Transl Oncol. 2016;18:798–804.

    Article  CAS  PubMed  Google Scholar 

  20. Wu PC, Lu JW, Yang JY, Lin IH, Ou DL, Lin YH, et al. H3K9 histone methyltransferase, KMT1E/SETDB1, cooperates with the SMAD2/3 pathway to suppress lung cancer metastasis. Cancer Res. 2014;74:7333–43.

    Article  CAS  PubMed  Google Scholar 

  21. Saini P, Courtneidge SA. Tks adaptor proteins at a glance. J Cell Sci. 2018;131:jcs203661.

  22. Li CM, Chen G, Dayton TL, Kim-Kiselak C, Hoersch S, Whittaker CA, et al. Differential Tks5 isoform expression contributes to metastatic invasion of lung adenocarcinoma. Genes Dev. 2013;27:1557–67.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Li CM, Gocheva V, Oudin MJ, Bhutkar A, Wang SY, Date SR, et al. Foxa2 and Cdx2 cooperate with Nkx2-1 to inhibit lung adenocarcinoma metastasis. Genes Dev. 2015;29:1850–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Basseres DS, D’Alo F, Yeap BY, Lowenberg EC, Gonzalez DA, Yasuda H, et al. Frequent downregulation of the transcription factor Foxa2 in lung cancer through epigenetic silencing. Lung Cancer. 2012;77:31–7.

    Article  PubMed  Google Scholar 

  25. Halmos B, Basseres DS, Monti S, D’Alo F, Dayaram T, Ferenczi K, et al. A transcriptional profiling study of CCAAT/enhancer binding protein targets identifies hepatocyte nuclear factor 3 beta as a novel tumor suppressor in lung cancer. Cancer Res. 2004;64:4137–47.

    Article  CAS  PubMed  Google Scholar 

  26. Sun L, Fang J. Epigenetic regulation of epithelial-mesenchymal transition. Cell Mol Life Sci. 2016;73:4493–515.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Lowy CM, Oskarsson T. Tenascin C in metastasis: a view from the invasive front. Cell Adh Migr. 2015;9:112–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Nyren-Erickson EK, Jones JM, Srivastava DK, Mallik S. A disintegrin and metalloproteinase-12 (ADAM12): function, roles in disease progression, and clinical implications. Biochim Biophys Acta. 2013;1830:4445–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Abram CL, Seals DF, Pass I, Salinsky D, Maurer L, Roth TM, et al. The adaptor protein fish associates with members of the ADAMs family and localizes to podosomes of Src-transformed cells. J Biol Chem. 2003;278:16844–51.

    Article  CAS  PubMed  Google Scholar 

  30. Eckert MA, Santiago-Medina M, Lwin TM, Kim J, Courtneidge SA, Yang J. ADAM12 induction by Twist1 promotes tumor invasion and metastasis via regulation of invadopodia and focal adhesions. J Cell Sci. 2017;130:2036–48.

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Hawkins AG, Julian CM, Konzen S, Treichel S, Lawlor ER, Bailey KM. Microenvironmental factors drive tenascin C and Src cooperation to promote invadopodia formation in ewing sarcoma. Neoplasia. 2019;21:1063–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Eddy RJ, Weidmann MD, Sharma VP, Condeelis JS. Tumor cell invadopodia: invasive protrusions that orchestrate metastasis. Trends Cell Biol. 2017;27:595–607.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Bowden ET, Onikoyi E, Slack R, Myoui A, Yoneda T, Yamada KM, et al. Co-localization of cortactin and phosphotyrosine identifies active invadopodia in human breast cancer cells. Exp Cell Res. 2006;312:1240–53.

    Article  CAS  PubMed  Google Scholar 

  34. Pelaez R, Morales X, Salvo E, Garasa S, Ortiz de Solorzano C, Martinez A, et al. beta3 integrin expression is required for invadopodia-mediated ECM degradation in lung carcinoma cells. PLoS ONE. 2017;12:e0181579.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  35. Bowden ET, Coopman PJ, Mueller SC. Invadopodia: unique methods for measurement of extracellular matrix degradation in vitro. Methods Cell Biol. 2001;63:613–27.

    Article  CAS  PubMed  Google Scholar 

  36. Fei Q, Yang X, Jiang H, Wang Q, Yu Y, Yu Y, et al. SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells. Genome Res. 2015;25:1325–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Leung D, Du T, Wagner U, Xie W, Lee AY, Goyal P, et al. Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1. Proc Natl Acad Sci USA. 2014;111:6690–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Li H, Rauch T, Chen ZX, Szabo PE, Riggs AD, Pfeifer GP. The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. J Biol Chem. 2006;281:19489–500.

    Article  CAS  PubMed  Google Scholar 

  39. Holemon H, Korshunova Y, Ordway JM, Bedell JA, Citek RW, Lakey N, et al. MethylScreen: DNA methylation density monitoring using quantitative PCR. Biotechniques. 2007;43:683–93.

    Article  CAS  PubMed  Google Scholar 

  40. Bahar Halpern K, Vana T, Walker MD. Paradoxical role of DNA methylation in activation of FoxA2 gene expression during endoderm development. J Biol Chem. 2014;289:23882–92.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Kokura K, Sun L, Bedford MT, Fang J. Methyl-H3K9-binding protein MPP8 mediates E-cadherin gene silencing and promotes tumour cell motility and invasion. EMBO J. 2010;29:3673–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Winslow MM, Dayton TL, Verhaak RG, Kim-Kiselak C, Snyder EL, Feldser DM, et al. Suppression of lung adenocarcinoma progression by Nkx2-1. Nature. 2011;473:101–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Wan H, Kaestner KH, Ang SL, Ikegami M, Finkelman FD, Stahlman MT, et al. Foxa2 regulates alveolarization and goblet cell hyperplasia. Development. 2004;131:953–64.

    Article  CAS  PubMed  Google Scholar 

  44. Tang Y, Shu G, Yuan X, Jing N, Song J. FOXA2 functions as a suppressor of tumor metastasis by inhibition of epithelial-to-mesenchymal transition in human lung cancers. Cell Res. 2011;21:316–26.

    Article  CAS  PubMed  Google Scholar 

  45. Zhang Z, Yang C, Gao W, Chen T, Qian T, Hu J, et al. FOXA2 attenuates the epithelial to mesenchymal transition by regulating the transcription of E-cadherin and ZEB2 in human breast cancer. Cancer Lett. 2015;361:240–50.

    Article  CAS  PubMed  Google Scholar 

  46. Wang B, Liu G, Ding L, Zhao J, Lu Y. FOXA2 promotes the proliferation, migration and invasion, and epithelial mesenchymal transition in colon cancer. Exp Ther Med. 2018;16:133–40.

    PubMed  PubMed Central  Google Scholar 

  47. Naciri I, Laisne M, Ferry L, Bourmaud M, Gupta N, Di Carlo S, et al. Genetic screens reveal mechanisms for the transcriptional regulation of tissue-specific genes in normal cells and tumors. Nucleic Acids Res. 2019;47:3407–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Liu J, Yu Z, Xiao Y, Meng Q, Wang Y, Chang W. Coordination of FOXA2 and SIRT6 suppresses the hepatocellular carcinoma progression through ZEB2 inhibition. Cancer Manag Res. 2018;10:391–402.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Fuks F. DNA methylation and histone modifications: teaming up to silence genes. Curr Opin Genet Dev. 2005;15:490–5.

    Article  CAS  PubMed  Google Scholar 

  50. Smallwood A, Esteve PO, Pradhan S, Carey M. Functional cooperation between HP1 and DNMT1 mediates gene silencing. Genes Dev. 2007;21:1169–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Sarraf SA, Stancheva I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell. 2004;15:595–605.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank Dr. Tyler Jacks for murine lung adenocarcinoma cell lines, Dr. Shengyu Yang for technical assistance with invadopodia assays, Dr. David Goodrich for constructive discussion and suggestions and support from Roswell Park Comprehensive Cancer Center (RPCCC) Shared Resources, including BIOINFO, GSR, TISR, and LASR. This project was supported, in part, by grants from the NIH (CA172774) and Roswell Park Alliance Foundation (all to JF), and by RPCCC and NCI center grant P30CA016056.

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  1. Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA

    Shuhei Ueshima & Jia Fang

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  1. Shuhei Ueshima
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JF conceived the project, designed the experiments, and wrote the paper. SU carried out the experiments and analyzed data.

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Correspondence to Jia Fang.

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Ueshima, S., Fang, J. Histone H3K9 methyltransferase SETDB1 augments invadopodia formation to promote tumor metastasis. Oncogene 41, 3370–3380 (2022). https://doi.org/10.1038/s41388-022-02345-3

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