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The lncRNA BORG facilitates the survival and chemoresistance of triple-negative breast cancers

Oncogene (2018) | Download Citation

Abstract

Disseminated breast cancer cells employ adaptive molecular responses following cytotoxic therapeutic insult which promotes their survival and subsequent outgrowth. Here we demonstrate that expression of the pro-metastatic lncRNA BORG (BMP/OP-Responsive Gene) is greatly induced within triple-negative breast cancer (TNBC) cells subjected to environmental and chemotherapeutic stresses commonly faced by TNBC cells throughout the metastatic cascade. This stress-mediated induction of BORG expression fosters the survival of TNBC cells and renders them resistant to the cytotoxic effects of doxorubicin both in vitro and in vivo. The chemoresistant traits of BORG depend upon its robust activation of the NF-κB signaling axis via a novel BORG-mediated feed-forward signaling loop, and via its ability to bind and activate RPA1. Indeed, genetic and pharmacologic inhibition of NF-κB signaling or the DNA-binding activity of RPA1 abrogates the pro-survival features of BORG and renders BORG-expressing TNBCs sensitive to doxorubicin-induced cytotoxicity. These findings suggest that therapeutic targeting of BORG or its downstream molecular effectors may provide a novel means to alleviate TNBC recurrence.

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Data availability

All sequencing data provided herein have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) and can be accessed through the GEO Series accession number GSE116656. All additional data are available from the corresponding authors upon request.

References

  1. 1.

    Torre LA, Islami F, Siegel RL, Ward EM, Jemal A. Global cancer in women: burden and trends. Cancer Epidemiol Biomark Prev. 2017;26:444–57.

  2. 2.

    Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA. 2001;98:10869–74.

  3. 3.

    Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA. 2003;100:8418–23.

  4. 4.

    Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, et al. Molecular portraits of human breast tumours. Nature. 2000;406:747–52.

  5. 5.

    Alluri P, Newman LA. Basal-like and triple-negative breast cancers: searching for positives among many negatives. Surg Oncol Clin N Am. 2014;23:567–77.

  6. 6.

    Dent R, Trudeau M, Pritchard KI, Hanna WM, Kahn HK, Sawka CA, et al. Triple-negative breast cancer: clinical features and patterns of recurrence. Clin Cancer Res. 2007;13:4429–34.

  7. 7.

    Chiang AC, Massague J. Molecular basis of metastasis. N Engl J Med. 2008;359:2814–23.

  8. 8.

    Vanharanta S, Massague J. Origins of metastatic traits. Cancer Cell. 2013;24:410–21.

  9. 9.

    Luzzi KJ, MacDonald IC, Schmidt EE, Kerkvliet N, Morris VL, Chambers AF, et al. Multistep nature of metastatic inefficiency: dormancy of solitary cells after successful extravasation and limited survival of early micrometastases. Am J Pathol. 1998;153:865–73.

  10. 10.

    Klein CA. Framework models of tumor dormancy from patient-derived observations. Curr Opin Genet Dev. 2011;21:42–49.

  11. 11.

    Senft D, Ronai ZE. Adaptive stress responses during tumor metastasis and dormancy. Trends Cancer. 2016;2:429–42.

  12. 12.

    Lambert AW, Pattabiraman DR, Weinberg RA. Emerging biological principles of metastasis. Cell. 2017;168:670–91.

  13. 13.

    Tiligada E. Chemotherapy: induction of stress responses. Endocr Relat Cancer. 2006;13(Suppl 1):S115–124.

  14. 14.

    Acharyya S, Oskarsson T, Vanharanta S, Malladi S, Kim J, Morris PG, et al. A CXCL1 paracrine network links cancer chemoresistance and metastasis. Cell. 2012;150:165–78.

  15. 15.

    Holohan C, Van Schaeybroeck S, Longley DB, Johnston PG. Cancer drug resistance: an evolving paradigm. Nat Rev Cancer. 2013;13:714–26.

  16. 16.

    Hoesel B, Schmid JA. The complexity of NF-kappaB signaling in inflammation and cancer. Mol Cancer. 2013;12:86.

  17. 17.

    Hayden MS, Ghosh S. NF-kappaB, the first quarter-century: remarkable progress and outstanding questions. Genes Dev. 2012;26:203–34.

  18. 18.

    Godwin P, Baird AM, Heavey S, Barr MP, O’Byrne KJ, Gately K. Targeting nuclear factor-kappa B to overcome resistance to chemotherapy. Front Oncol. 2013;3:120.

  19. 19.

    Montagut C, Tusquets I, Ferrer B, Corominas JM, Bellosillo B, Campas C, et al. Activation of nuclear factor-kappa B is linked to resistance to neoadjuvant chemotherapy in breast cancer patients. Endocr Relat Cancer. 2006;13:607–16.

  20. 20.

    Schmitt AM, Chang HY. Long noncoding RNAs in cancer pathways. Cancer Cell. 2016;29:452–63.

  21. 21.

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

  22. 22.

    Di Gesualdo F, Capaccioli S, Lulli M. A pathophysiological view of the long non-coding RNA world. Oncotarget. 2014;5:10976–96.

  23. 23.

    Malhotra A, Jain M, Prakash H, Vasquez KM, Jain A. The regulatory roles of long non-coding RNAs in the development of chemoresistance in breast cancer. Oncotarget. 2017;8:110671–84.

  24. 24.

    Gooding AJ, Zhang B, Jahanbani FK, Gilmore HL, Chang JC, Valadkhan S, et al. The lncRNA BORG drives breast cancer metastasis and disease recurrence. Sci Rep. 2017;7:12698.

  25. 25.

    Yap WT, Salvay DM, Silliman MA, Zhang X, Bannon ZG, Kaufman DB, et al. Collagen IV-modified scaffolds improve islet survival and function and reduce time to euglycemia. Tissue Eng Part A. 2013;19:2361–72.

  26. 26.

    Somaiah C, Kumar A, Mawrie D, Sharma A, Patil SD, Bhattacharyya J, et al. Collagen promotes higher adhesion, survival and proliferation of mesenchymal stem cells. PLoS ONE. 2015;10:e0145068.

  27. 27.

    Valadkhan S, Valencia-Hipolito A. lncRNAs in stress response. Curr Top Microbiol Immunol. 2016;394:203–36.

  28. 28.

    Zhang B, Gunawardane L, Niazi F, Jahanbani FK, Chen X, Valadkhan S. A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA. Mol Cell Biol. 2014;34:2318–29.

  29. 29.

    Takeda K, Ichijo H, Fujii M, Mochida Y, Saitoh M, Nishitoh H, et al. Identification of a novel bone morphogenetic protein-responsive gene that may function as a noncoding RNA. J Biol Chem. 1998;273:17079–85.

  30. 30.

    Zanotto-Filho A, Masamsetti VP, Loranc E, Tonapi SS, Gorthi A, Bernard X, et al. Alkylating agent-induced NRF2 blocks endoplasmic reticulum stress-mediated apoptosis via control of glutathione pools and protein thiol homeostasis. Mol Cancer Ther. 2016;15:3000–14.

  31. 31.

    Lupertz R, Watjen W, Kahl R, Chovolou Y. Dose- and time-dependent effects of doxorubicin on cytotoxicity, cell cycle and apoptotic cell death in human colon cancer cells. Toxicology. 2010;271:115–21.

  32. 32.

    Tyagi AK, Singh RP, Agarwal C, Chan DC, Agarwal R. Silibinin strongly synergizes human prostate carcinoma DU145 cells to doxorubicin-induced growth Inhibition, G2-M arrest, and apoptosis. Clin Cancer Res. 2002;8:3512–9.

  33. 33.

    DiPaola RS. To arrest or not to G(2)-M Cell-cycle arrest: commentary re: A. K. Tyagi et al., Silibinin strongly synergizes human prostate carcinoma DU145 cells to doxorubicin-induced growth inhibition, G(2)-M arrest, and apoptosis. Clin. cancer res., 8: 3512-3519, 2002. Clin Cancer Res. 2002;8:3311–4.

  34. 34.

    Ling YH, el-Naggar AK, Priebe W, Perez-Soler R. Cell cycle-dependent cytotoxicity, G2/M phase arrest, and disruption of p34cdc2/cyclin B1 activity induced by doxorubicin in synchronized P388 cells. Mol Pharmacol. 1996;49:832–41.

  35. 35.

    Neil JR, Schiemann WP. Altered TAB1:I kappaB kinase interaction promotes transforming growth factor beta-mediated nuclear factor-kappaB activation during breast cancer progression. Cancer Res. 2008;68:1462–70.

  36. 36.

    Neil JR, Tian M, Schiemann WP. X-linked inhibitor of apoptosis protein and its E3 ligase activity promote transforming growth factor-beta-mediated nuclear factor-kappaB activation during breast cancer progression. J Biol Chem. 2009;284:21209–17.

  37. 37.

    Tong AJ, Liu X, Thomas BJ, Lissner MM, Baker MR, Senagolage MD, et al. A stringent systems approach uncovers gene-specific mechanisms regulating inflammation. Cell. 2016;165:165–79.

  38. 38.

    Furlow PW, Zhang S, Soong TD, Halberg N, Goodarzi H, Mangrum C, et al. Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival. Nat Cell Biol. 2015;17:943–52.

  39. 39.

    Gomis RR, Alarcon C, Nadal C, Van Poznak C, Massague J. C/EBPbeta at the core of the TGFbeta cytostatic response and its evasion in metastatic breast cancer cells. Cancer Cell. 2006;10:203–14.

  40. 40.

    Piva R, Belardo G, Santoro MG. NF-kappaB: a stress-regulated switch for cell survival. Antioxid Redox Signal. 2006;8:478–86.

  41. 41.

    Tornatore L, Sandomenico A, Raimondo D, Low C, Rocci A, Tralau-Stewart C, et al. Cancer-selective targeting of the NF-kappaB survival pathway with GADD45beta/MKK7 inhibitors. Cancer Cell. 2014;26:495–508.

  42. 42.

    Wullaert A, Bonnet MC, Pasparakis M. NF-kappaB in the regulation of epithelial homeostasis and inflammation. Cell Res. 2011;21:146–58.

  43. 43.

    Ahmed KM, Cao N, Li JJ. HER-2 and NF-kappaB as the targets for therapy-resistant breast cancer. Anticancer Res. 2006;26:4235–43.

  44. 44.

    Khan S, Lopez-Dee Z, Kumar R, Ling J. Activation of NFkB is a novel mechanism of pro-survival activity of glucocorticoids in breast cancer cells. Cancer Lett. 2013;337:90–95.

  45. 45.

    Boehm JS, Zhao JJ, Yao J, Kim SY, Firestein R, Dunn IF, et al. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell. 2007;129:1065–79.

  46. 46.

    Brown K, Gerstberger S, Carlson L, Franzoso G, Siebenlist U. Control of I kappa B-alpha proteolysis by site-specific, signal-induced phosphorylation. Science. 1995;267:1485–8.

  47. 47.

    Israel A. The IKK complex, a central regulator of NF-kappaB activation. Cold Spring Harb Perspect Biol. 2010;2:a000158.

  48. 48.

    Yuan Y, Hilliard G, Ferguson T, Millhorn DE. Cobalt inhibits the interaction between hypoxia-inducible factor-alpha and von Hippel-Lindau protein by direct binding to hypoxia-inducible factor-alpha. J Biol Chem. 2003;278:15911–6.

  49. 49.

    Gupta SC, Sundaram C, Reuter S, Aggarwal BB. Inhibiting NF-kappaB activation by small molecules as a therapeutic strategy. Biochim Biophys Acta. 2010;1799:775–87.

  50. 50.

    Kouroukis TC, Baldassarre FG, Haynes AE, Imrie K, Reece DE, Cheung MC. Bortezomib in multiple myeloma: systematic review and clinical considerations. Curr Oncol. 2014;21:e573–603.

  51. 51.

    Paramore A, Frantz S. Bortezomib. Nat Rev Drug Discov. 2003;2:611–2.

  52. 52.

    Lu S, Wang J. The resistance mechanisms of proteasome inhibitor bortezomib. Biomark Res. 2013;1:13.

  53. 53.

    Lopez JS, Banerji U. Combine and conquer: challenges for targeted therapy combinations in early phase trials. Nat Rev Clin Oncol. 2017;14:57–66.

  54. 54.

    Zhao M, Geng R, Guo X, Yuan R, Zhou X, Zhong Y, et al. PCAF/GCN5-mediated acetylation of RPA1 promotes nucleotide excision repair. Cell Rep. 2017;20:1997–2009.

  55. 55.

    Haring SJ, Mason AC, Binz SK, Wold MS. Cellular functions of human RPA1. Multiple roles of domains in replication, repair, and checkpoints. J Biol Chem. 2008;283:19095–111.

  56. 56.

    Shuck SC, Turchi JJ. Targeted inhibition of replication protein A reveals cytotoxic activity, synergy with chemotherapeutic DNA-damaging agents, and insight into cellular function. Cancer Res. 2010;70:3189–98.

  57. 57.

    Lakhotia SC. Long non-coding RNAs coordinate cellular responses to stress. Wiley Interdiscip Rev Rna. 2012;3:779–96.

  58. 58.

    Jezierska-Drutel A, Rosenzweig SA, Neumann CA. Role of oxidative stress and the microenvironment in breast cancer development and progression. Adv Cancer Res. 2013;119:107–25.

  59. 59.

    White E, Mehnert JM, Chan CS. Autophagy, metabolism, and cancer. Clin Cancer Res. 2015;21:5037–46.

  60. 60.

    Mahadevan NR, Zanetti M. Tumor stress inside out: cell-extrinsic effects of the unfolded protein response in tumor cells modulate the immunological landscape of the tumor microenvironment. J Immunol. 2011;187:4403–9.

  61. 61.

    Catalano V, Turdo A, Di Franco S, Dieli F, Todaro M, Stassi G. Tumor and its microenvironment: a synergistic interplay. Semin Cancer Biol. 2013;23:522–32.

  62. 62.

    Victorino VJ, Pizzatti L, Michelletti P, Panis C. Oxidative stress, redox signaling and cancer chemoresistance: putting together the pieces of the puzzle. Curr Med Chem. 2014;21:3211–26.

  63. 63.

    Huang Z, Zhou L, Chen Z, Nice EC, Huang C. Stress management by autophagy: Implications for chemoresistance. Int J Cancer. 2016;139:23–32.

  64. 64.

    Baral E, Auer G. In vitro effect of doxorubicin on non-proliferating and proliferating epithelial cells. Int J Radiat Oncol Biol Phys. 1990;19:963–5.

  65. 65.

    Li S, Kennedy M, Payne S, Kennedy K, Seewaldt VL, Pizzo SV, et al. Model of tumor dormancy/recurrence after short-term chemotherapy. PLoS One. 2014;9:e98021.

  66. 66.

    Wan F, Lenardo MJ. Specification of DNA binding activity of NF-kappaB proteins. Cold Spring Harb Perspect Biol. 2009;1:a000067.

  67. 67.

    Zhong H, May MJ, Jimi E, Ghosh S. The phosphorylation status of nuclear NF-kappa B determines its association with CBP/p300 or HDAC-1. Mol Cell. 2002;9:625–36.

  68. 68.

    Huang B, Yang XD, Zhou MM, Ozato K, Chen LF. Brd4 coactivates transcriptional activation of NF-kappaB via specific binding to acetylated RelA. Mol Cell Biol. 2009;29:1375–87.

  69. 69.

    Mao X, Su Z, Mookhtiar AK. Long non-coding RNA: a versatile regulator of the nuclear factor-kappaB signalling circuit. Immunology. 2017;150:379–88.

  70. 70.

    Li CH, Chen Y. Targeting long non-coding RNAs in cancers: progress and prospects. Int J Biochem Cell Biol. 2013;45:1895–910.

  71. 71.

    Wendt MK, Taylor MA, Schiemann BJ, Schiemann WP. Downregulation of epithelial cadherin is required to initiate metastatic outgrowth of breast cancer. Mol Biol Cell. 2011;22:2423–35.

  72. 72.

    Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014;343:84–87.

  73. 73.

    Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E. CHOPCHOPv2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res. 2016;44:W272–276.

  74. 74.

    Guzman C, Bagga M, Kaur A, Westermarck J, Abankwa D. ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays. PLoS One. 2014;9:e92444.

  75. 75.

    Courilleau C, Chailleux C, Jauneau A, Grimal F, Briois S, Boutet-Robinet E, et al. The chromatin remodeler p400 ATPase facilitates Rad51-mediated repair of DNA double-strand breaks. J Cell Biol. 2012;199:1067–81.

  76. 76.

    Boutet-Robinet E, Trouche D, Canitrot Y. Neutral comet assay. Bio Protoc. 2013;3:12–17.

  77. 77.

    Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105–11.

  78. 78.

    Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511–5.

  79. 79.

    Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102:15545–50.

  80. 80.

    Faul F, Erdfelder E, Buchner A, Lang AG. Statistical power analyses using G*Power 3.1: tests for correlation and regression analyses. Behav Res Methods. 2009;41:1149–60.

  81. 81.

    Farre D, Roset R, Huerta M, Adsuara JE, Rosello L, Alba MM, et al. Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. Nucleic Acids Res. 2003;31:3651–3.

  82. 82.

    Messeguer X, Escudero R, Farre D, Nunez O, Martinez J, Alba MM. PROMO: detection of known transcription regulatory elements using species-tailored searches. Bioinformatics. 2002;18:333–4.

  83. 83.

    Goldman M, Craft B, Brooks A, Zhu J, Haussler D. The UCSC Xena Platform for cancer genomics data visualization and interpretation. BioRxiv. 2018. https://doi.org/10.1101/326470.

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Acknowledgements

Members of the Schiemann Laboratory are thanked for critical comments and reading of the manuscript. We thank Dr. Ricky Chan for assistance in our analyses of RNA-seq data. We also acknowledge the expertise provided by members of the Case Comprehensive Cancer Center’s Core Facilities, including the Gene Expression & Genotyping Core, the Imaging Research Core, Tissue Resources Core, and the Genomics Core. Research support was provided in part by the National Institutes of Health to W.P.S. (CA129359, CA177069, and CA194518) and A.J.G (T32GM007250 and F30CA203233). Additional support was graciously provided by the METAvivor Foundation (W.P.S.), and by pilot funding from the Case Comprehensive Cancer Center’s Research Innovation Fund, which is supported by the Case Council and Friends of the Case Comprehensive Cancer Center (W.P.S. and S.V.).

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Affiliations

  1. Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA

    • Alex J. Gooding
    • , Abigail Beard
    •  & William P. Schiemann
  2. Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, 44106, USA

    • Bing Zhang
    • , Lalith Gunawardane
    •  & Saba Valadkhan

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Contributions

A.J.G., S.V. and W.P.S. conceived and designed the study, as well as interpreted the findings. A.J.G. carried out the molecular, cellular, and in vivo analyses with assistance from B.Z., L.G, and A.B. A.J.G. drafted the manuscript, which was revised and edited by A.J.G., S.V. and W.P.S. All authors read, commented, and approved the final version of the manuscript.

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The authors declare that they have no conflict of interest.

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Correspondence to Saba Valadkhan or William P. Schiemann.

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https://doi.org/10.1038/s41388-018-0586-4