Cross-Talk Between circRNAs and mRNAs Modulates MiRNA-mediated Circuits and Affects Melanoma Plasticity

  • Maria Rita Fumagalli
  • Maria Chiara Lionetti
  • Stefano Zapperi
  • Caterina A. M. La PortaEmail author
Original Article


CircularRNAs (circRNAs) are non-coding RNAs which compete for microRNA (miRNA) binding, influencing the abundance and stability of other RNA species. Herein we have investigated the effect of circRNAs on the mir200-ZEB1 feedback loop in relationship with the aggressiveness of human melanoma cells. We first compared the level of expression of key factors in the mir200-ZEB1 feedback loop in primary human melanoma cells compared with their matching metastatic one and found a correlation between the aggressiveness of the cells and the level of expression of ZEB1 and SNAI1. We also analyzed factors in the mir200-ZEB1 feedback loop, including circZEB1, during the phenotypic switching of human melanoma cells. Our results showed a correlation between the level of ZEB1 and SNAI1 and the fraction of cancer stem cells in the population. The level of circZEB1 was, however, consistently high during the entire phenotypic transformation. To understand this result we propose a mathematical model of the regulatory circuit. According to the model, the experimental observations can be explained by the presence of a back-splicing factor limiting circRNA production.


circRNA ZEB1 Melanoma Phenotypic switching 



The project was supported by funded from the Center for Complexity and Biosystems of UniMI. The research leading to these results was funded by AIRC under IG2018-ID 21558 project-PI Pusch Michael.

Supplementary material

12307_2019_230_MOESM1_ESM.pdf (24 kb)
(PDF 23.6 KB)
12307_2019_230_MOESM2_ESM.pdf (23 kb)
(PDF 23.1 KB)
12307_2019_230_MOESM3_ESM.pdf (9 kb)
(PDF 8.83 KB)


  1. 1.
    La Porta CAM, Zapperi S (2018) Semin Cancer Biol 53:42. CrossRefPubMedGoogle Scholar
  2. 2.
    La Porta CAM, Zapperi S (2017) Semin Cancer Biol 44:3. CrossRefPubMedGoogle Scholar
  3. 3.
    Kreso A, O’Brien CA, van Galen P, Gan OI, Notta F, Brown AMK, Ng K, Ma J, Wienholds E, Dunant C, Pollett A, Gallinger S, McPherson J, Mullighan CG, Shibata D, Dick JE (2013) Science 339(6119):543. CrossRefPubMedGoogle Scholar
  4. 4.
    Sharma SV, Lee DY, Li B, Quinlan MP, Takahashi F, Maheswaran S, McDermott U, Azizian N, Zou L, Fischbach MA, Wong KK, Brandstetter K, Wittner B, Ramaswamy S, Classon M, Settleman J (2010) Cell 141(1):69. CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Easwaran H, Tsai HC, Baylin SB (2014) Mol Cell 54(5):716. CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Sellerio AL, Ciusani E, Ben-Moshe NB, Coco S, Piccinini A, Myers CR, Sethna JP, Giampietro C, Zapperi S, La Porta CAM (2015) Sci Rep 5:15464. CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Jia Chan J, Tay Y (2018) Int J Mol Sci 19:1310. CrossRefPubMedCentralGoogle Scholar
  8. 8.
    Chen LL (2016) Nat Rev Mol Cell Biol 17(4):205. Cited By 18CrossRefGoogle Scholar
  9. 9.
    Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441):333. Nature Publishing GroupCrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, Marzluff WF, Sharpless NE (2013) Circular RNAs are abundant, conserved, and associated with ALU repeats. Rna 19(2):141. CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Hansen T, Kjems J, Damgaard CK (2013) Circular RNA and miR-7 in cancer. Cancer Res 73(18):5609. CrossRefPubMedGoogle Scholar
  12. 12.
    li Y, Zheng Q, Bao C, Li S, Guo W, Zhao J, Di C, Gu J, He X, Huang S (2015) Cell Res 25. CrossRefGoogle Scholar
  13. 13.
    Memczak S, Papavasileiou P, Peters O, Rajewsky N (2015) Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood. PloS one 10(10):e0141214. CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Huang S, Yang B, Chen B, Bliim N, Ueberham U, Arendt T, Janitz M (2017) The emerging role of circular RNAs in transcriptome regulation. Genomics 109(5-6):401. CrossRefPubMedGoogle Scholar
  15. 15.
    Chen J, Li Y, Zheng Q, Bao C, He J, Chen B, Lyu D, Zheng B, Xu Y, Long Z et al (2017) Circular RNA profile identifies circPVT1 as a proliferative factor and prognostic marker in gastric cancer. Cancer Lett 388:208. CrossRefPubMedGoogle Scholar
  16. 16.
    Li P, Chen S, Chen H, Mo X, Li T, Shao Y, Xiao B, Guo J (2015) Using circular RNA as a novel type of biomarker in the screening of gastric cancer. Clinica Chimica Acta 444:132. CrossRefGoogle Scholar
  17. 17.
    Xie H, Ren X, Xin S, Lan X, Lu G, Lin Y, Yang S, Zeng Z, Liao W, Ding YQ et al (2016) Emerging roles of circRNA_001569 targeting miR-145 in the proliferation and invasion of colorectal cancer. Oncotarget 7(18):26680. CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Zheng Q, Bao C, Guo W, Li S, Chen J, Chen B, Luo Y, Lyu D, Li Y, Shi G, Liang L, Gu J, He X, Huang S (2016) Nature Commun 7.
  19. 19.
    Fumagalli MR, Zapperi S, La Porta CA (2018) Impact of the cross-talk between circular and messenger RNAs on cell regulation. J Theor Biol 454:386. CrossRefPubMedGoogle Scholar
  20. 20.
    Salmena L, Poliseno L, Tay Y, Kats L, Paolo Pandolfi P (2011) Cell 146:353. CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Bosia C, Pagnani A, Zecchina R (2013) Modelling competing endogenous RNA networks. PLoS ONE 8(6):1. CrossRefGoogle Scholar
  22. 22.
    Figliuzzi M, Marinari E, De Martino A (2013) Biophys J 104:1203. CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Park SM, Gaur AB, Lengyel E, Peter ME (2008) Genes Dev 22:894. CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Burk U, Schubert J, Wellner U, Schmalhofer O, Vincan E, Spaderna S, Brabletz T (2008) EMBO Rep 9(6):582. CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Wang G, Guo X, Hong W, Liu Q, Wei T, Lu C, Gao L, Ye D, Zhou Y, Chen J, Wang J, Wu M, Liu H, Kang J (2013) Proc Natl Acad Sci USA 110(8):2858. CrossRefPubMedGoogle Scholar
  26. 26.
    Consortium TU (2015) Nucleic Acids Res 43:D204. CrossRefGoogle Scholar
  27. 27.
    Zerbino DR, Achuthan P, Akanni W, Ridwan Amode M, Barrell D, Bhai J, Billis K, Cummins C, Gall A, García Girón C, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kiang To J, Flicek P (2017) Nucleic Acids Res 46. CrossRefGoogle Scholar
  28. 28.
    Liu YC, Li J, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu SD, Huang CC, Cheng C, Liu CC, Huang HD (2015) Nucleic Acids Res 44. CrossRefGoogle Scholar
  29. 29.
    Glažar P, Papavasileiou P, Rajewsky N (2014) RNA (New York, NY) 20. CrossRefGoogle Scholar
  30. 30.
    Lu Y, Lu J, Li X, Zhu H, Fan X, Zhu S, Wang Y, Guo Q, Wang L, Huang Y, Zhu M, Wang Z (2014) BMC Cancer 14(1):85. CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Iliopoulos D, Polytarchou C, Hatziapostolou M, Kottakis F, Maroulakou I, Struhl K, Tsichlis P (2009) Sci Signal 2:ra62. CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Pichler M, Ress A, Winter E, Stiegelbauer V, Karbiener M, Schwarzenbacher D, Scheideler M, Ivan C, Jahn SW, Kiesslich T, Gerger A, Bauernhofer T, Calin G, Hoefler G (2014) Br J Cancer 110. CrossRefGoogle Scholar
  33. 33.
    Guan T, Dominguez CX, Amezquita RA, Laidlaw BJ, Cheng J, Henao-Mejia J, Williams A, Flavell RA, Lu J, Kaech SM (2018) J Exp Med 215(4):1153. CrossRefGoogle Scholar
  34. 34.
    Facchetti F, Previdi S, Ballarini M, Minucci S, Perego P, Porta C (2004) Apoptosis 9(5):573. CrossRefPubMedGoogle Scholar
  35. 35.
    Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Nucleic Acids Res 40:e115. CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden T (2009) BMC Bioinf 10(421). CrossRefGoogle Scholar
  37. 37.
    R Core Team R (2015) Language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
  38. 38.
    Grossman R, Heath AP, Ferretti V, Varmus HE, Lowy DR, Kibbe WA, Staudt LM (2016) N Engl J Med 375:1109. CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
  40. 40.
    Lu M, Jolly MK, Levine H, Onuchic JN, Ben-Jacob E (2013) MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination. Proc Natl Acad Sci 110(45):18144. CrossRefPubMedGoogle Scholar
  41. 41.
    Lu M, Jolly MK, Gomoto R, Huang B, Nelson Onuchic J, Ben-Jacob E (2013) J Phys Chem B 117. CrossRefGoogle Scholar
  42. 42.
    Hill L, Browne G, Tulchinsky E (2013) International journal of cancer. J Int Du Cancer 132. CrossRefGoogle Scholar
  43. 43.
    Preca BT, Bajdak K, Mock K, Sundararajan V, Pfannstiel J, Maurer J, Wellner U, Hopt UT, Brummer T, Brabletz S et al (2015) A self-enforcing CD44s/ZEB1 feedback loop maintains EMT and stemness properties in cancer cells. Int J Cancer 137(11):2566. CrossRefPubMedGoogle Scholar
  44. 44.
    Bail S, Swerdel M, Liu H, Jiao X, Goff LA, Hart RP, Kiledjian M (2010) Differential regulation of microRNA stability. Rna 16(5):1032. CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Rüegger S, Großhans H (2012) MicroRNA turnover: when, how, and why? Rüegger. Trends Biochem Sci 37(10):436. CrossRefPubMedGoogle Scholar
  46. 46.
    Zhang Z, Qin YW, Brewer G, Jing Q (2012) MicroRNA degradation and turnover: regulating the regulators. Wiley Interdisciplinary Reviews: RNA 3(4):593. CrossRefPubMedGoogle Scholar
  47. 47.
    Martirosyan A, De Martino A, Pagnani A, Marinari E (2017) Sci Rep 7.
  48. 48.
    Hunter JD (2007) Comput Sci Eng 9(3):90. CrossRefGoogle Scholar
  49. 49.
    Kalluri R, Weinberg R (2009) J Clin Invest 119:1420. CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Font-Clos F, Zapperi S, La Porta CA (2018) Topography of epithelial?mesenchymal plasticity. Proc Natl Acad Sci 115(23):5902. CrossRefPubMedGoogle Scholar
  51. 51.
    Jolly MK, Boareto M, Huang B, Jia D, Lu M, Ben-Jacob E, Onuchic JN, Levine H (2015) Front Oncol.
  52. 52.
    Kurahara H, Takao S, Maemura K, Mataki Y, Kuwahata T, Maeda K, Ding Q, Sakoda M, Iino S, Ishigami S et al (2012) Epithelial- mesenchymal transition and mesenchymal-epithelial transition via regulation of ZEB-1 and ZEB-2 expression in pancreatic cancer. J Surg Oncol 105(7):655. CrossRefPubMedGoogle Scholar
  53. 53.
    Richard G, Dalle S, Monet MA, Ligier M, Boespflug A, Pommier RM, de la Fouchardière A, Perier-Muzet M, Depaepe L, Barnault R et al (2016) ZEB1-mediated melanoma cell plasticity enhances resistance to MAPK inhibitors. EMBO Mol Med 8(10):1143. CrossRefPubMedPubMedCentralGoogle Scholar
  54. 54.
    Sakata J, Utsumi F, Suzuki S, Niimi K, Yamamoto E, Shibata K, Senga T, Kikkawa F, Kajiyama H (2017) Inhibition of ZEB1 leads to inversion of metastatic characteristics and restoration of paclitaxel sensitivity of chronic chemoresistant ovarian carcinoma cells. Oncotarget 8(59):99482. CrossRefPubMedPubMedCentralGoogle Scholar
  55. 55.
    Kahlert C, Lahes S, Radhakrishnan P, Dutta S, Mogler C, Herpel E, Brand K, Steinert G, Schneider M, Mollenhauer M et al (2011) Overexpression of ZEB2 at the invasion front of colorectal cancer is an independent prognostic marker and regulates tumor invasion in vitro. Clinical Cancer Res 17(24):7654. CrossRefGoogle Scholar
  56. 56.
    Eger A, Aigner K, Sonderegger S, Dampier B, Oehler S, Schreiber M, Berx G, Cano A, Beug H, Foisner R (2005) DeltaEF1 is a transcriptional repressor of E-cadherin and regulates epithelial plasticity in breast cancer cells. Oncogene 24(14):2375. CrossRefPubMedGoogle Scholar
  57. 57.
    Kristensen L, Hansen T, Venø M, Kjems J (2018) Circular RNAs in cancer: opportunities and challenges in the field. Oncogene 37(5):555. CrossRefPubMedGoogle Scholar
  58. 58.
    Shang X, Li G, Liu H, Li T, Liu J, Zhao Q, Wang C (2016) Comprehensive circular RNA profiling reveals that hsa_circ_0005075, a new circular RNA biomarker, is involved in hepatocellular crcinoma development. Medicine 95(22). CrossRefGoogle Scholar
  59. 59.
    Sand M, Bechara FG, Gambichler T, Sand D, Bromba M, Hahn SA, Stockfleth E, Hessam S (2016) Circular RNA expression in cutaneous squamous cell carcinoma. J Dermatol Sci 83(3): 210. CrossRefPubMedGoogle Scholar
  60. 60.
    Jiang LH, Sun DW, Hou JC, Ji ZL et al (2018) CircRNA: a novel type of biomarker for cancer. Breast Cancer 25(1):1. CrossRefPubMedGoogle Scholar
  61. 61.
    Gong Y, et al. (2018) Circ-ZEB1.33 promotes the proliferation of human HCC by sponging miR-200a-3p and upregulating CDK6. Cancer Cell Int 18(1):116. CrossRefPubMedPubMedCentralGoogle Scholar
  62. 62.
    Starke S, Jost I, Rossbach O, Schneider T, Schreiner S, Hung LH, Bindereif A (2015) Exon circularization requires canonical splice signals. Cell Rep 10(1):103. CrossRefPubMedGoogle Scholar
  63. 63.
    Conn SJ, Pillman KA, Toubia J, Conn VM, Salmanidis M, Phillips CA, Roslan S, Schreiber AW, Gregory PA, Goodall GJ (2015) The RNA binding protein quaking regulates formation of circRNAs. Cell 160(6):1125. CrossRefPubMedGoogle Scholar
  64. 64.
    Chen LL, Yang L (2015) Regulation of circRNA biogenesis. RNA Biology 12(4):381. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Consiglio Nazionale delle RicercheIstituto di BiofisicaMilanoItaly
  2. 2.Center for Complexity and Biosystems, Department of Environmental Science and PolicyUniversity of MilanMilanoItaly
  3. 3.Center for Complexity and Biosystems, Department of PhysicsUniversity of MilanoMilanoItaly
  4. 4.CNR - Consiglio Nazionale delle RicercheIstituto di Chimica della Materia Condensata e di Tecnologie per l’EnergiaMilanoItaly
  5. 5.Consiglio Nazionale delle RicercheIstituto di BiofisicaMilanoItaly

Personalised recommendations