Skip to main content

Thank you for visiting 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.

LINC00162 confers sensitivity to 5-Aza-2′-deoxycytidine via modulation of an RNA splicing protein, HNRNPH1


DNA demethylation therapy is now expanding from hematological tumors to solid tumors. To exploit its maximum efficacy, long-term treatment is needed, and stratification of sensitive patients is critically important. Here, we identified a long non-coding RNA, LINC00162, as highly and frequently expressed in gastric cancer cell lines sensitive to 5-aza-2′-deoxycytidine (5-aza-dC). Knockdown of LINC00162 decreased the sensitivity while its overexpression increased the sensitivity. In vivo experiments also showed that LINC00162 overexpression increased the sensitivity. LINC00162 enhanced cell cycle arrest and apoptosis induced by 5-aza-dC, but did not affect its DNA demethylation effect. Mechanistically, LINC00162 interacted with an RNA splicing protein, HNRNPH1, and decreased splicing of an anti-apoptotic splicing variant, BCL-XL. LINC00162 may have translational value to predict patients who will respond to 5-aza-dC.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5


  1. 1.

    Jones PA, Baylin SB. The epigenomics of cancer. Cell. 2007;128:683–92.

    CAS  Article  Google Scholar 

  2. 2.

    Esteller M. Epigenetics in cancer. N Engl J Med. 2008;358:1148–59.

    CAS  Article  Google Scholar 

  3. 3.

    Ushijima T. Detection and interpretation of altered methylation patterns in cancer cells. Nat Rev Cancer. 2005;5:223–31.

    CAS  Article  Google Scholar 

  4. 4.

    Niwa T, Tsukamoto T, Toyoda T, Mori A, Tanaka H, Maekita T, et al. Inflammatory processes triggered by Helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells. Cancer Res. 2010;70:1430–40.

    CAS  Article  Google Scholar 

  5. 5.

    Christman JK. 5-Azacytidine and 5-aza-2′-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy. Oncogene. 2002;21:5483–95.

    CAS  Article  Google Scholar 

  6. 6.

    Tsai HC, Li H, Van Neste L, Cai Y, Robert C, Rassool FV, et al. Transient low doses of DNA-demethylating agents exert durable antitumor effects on hematological and epithelial tumor cells. Cancer Cell. 2012;21:430–46.

    CAS  Article  Google Scholar 

  7. 7.

    Belinsky SA, Klinge DM, Stidley CA, Issa JP, Herman JG, March TH, et al. Inhibition of DNA methylation and histone deacetylation prevents murine lung cancer. Cancer Res. 2003;63:7089–93.

    CAS  PubMed  Google Scholar 

  8. 8.

    Niwa T, Toyoda T, Tsukamoto T, Mori A, Tatematsu M, Ushijima T. Prevention of Helicobacter pylori-induced gastric cancers in gerbils by a DNA demethylating agent. Cancer Prev Res (Phila). 2013;6:263–70.

    CAS  Article  Google Scholar 

  9. 9.

    Juttermann R, Li E, Jaenisch R. Toxicity of 5-aza-2′-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation. Proc Natl Acad Sci USA. 1994;91:11797–801.

    CAS  Article  Google Scholar 

  10. 10.

    Navada SC, Steinmann J, Lubbert M, Silverman LR. Clinical development of demethylating agents in hematology. J Clin Invest. 2014;124:40–46.

    CAS  Article  Google Scholar 

  11. 11.

    Sorm F, Vesely J. Effect of 5-aza-2′-deoxycytidine against leukemic and hemopoietic tissues in AKR mice. Neoplasma. 1968;15:339–43.

    CAS  PubMed  Google Scholar 

  12. 12.

    Jones PA, Taylor SM. Cellular differentiation, cytidine analogs and DNA methylation. Cell. 1980;20:85–93.

    CAS  Article  Google Scholar 

  13. 13.

    Kantarjian H, Oki Y, Garcia-Manero G, Huang X, O’Brien S, Cortes J, et al. Results of a randomized study of 3 schedules of low-dose decitabine in higher-risk myelodysplastic syndrome and chronic myelomonocytic leukemia. Blood. 2007;109:52–57.

    CAS  Article  Google Scholar 

  14. 14.

    Issa JP, Garcia-Manero G, Giles FJ, Mannari R, Thomas D, Faderl S, et al. Phase 1 study of low-dose prolonged exposure schedules of the hypomethylating agent 5-aza-2′-deoxycytidine (decitabine) in hematopoietic malignancies. Blood. 2004;103:1635–40.

    CAS  Article  Google Scholar 

  15. 15.

    Wijermans P, Lubbert M, Verhoef G, Bosly A, Ravoet C, Andre M, et al. Low-dose 5-aza-2′-deoxycytidine, a DNA hypomethylating agent, for the treatment of high-risk myelodysplastic syndrome: a multicenter phase II study in elderly patients. J Clin Oncol. 2000;18:956–62.

    CAS  Article  Google Scholar 

  16. 16.

    Kantarjian H, Issa JP, Rosenfeld CS, Bennett JM, Albitar M, DiPersio J, et al. Decitabine improves patient outcomes in myelodysplastic syndromes: results of a phase III randomized study. Cancer. 2006;106:1794–803.

    CAS  Article  Google Scholar 

  17. 17.

    Fenaux P, Mufti GJ, Hellstrom-Lindberg E, Santini V, Finelli C, Giagounidis A, et al. Efficacy of azacitidine compared with that of conventional care regimens in the treatment of higher-risk myelodysplastic syndromes: a randomised, open-label, phase III study. Lancet Oncol. 2009;10:223–32.

    CAS  Article  Google Scholar 

  18. 18.

    Sekeres MA, Othus M, List AF, Odenike O, Stone RM, Gore SD, et al. Randomized phase ii study of azacitidine alone or in combination with lenalidomide or with vorinostat in higher-risk myelodysplastic syndromes and chronic myelomonocytic leukemia: North American Intergroup Study SWOG S1117. J Clin Oncol. 2017;35:2745–53.

    CAS  Article  Google Scholar 

  19. 19.

    Yun S, Vincelette ND, Abraham I, Robertson KD, Fernandez-Zapico ME, Patnaik MM. Targeting epigenetic pathways in acute myeloid leukemia and myelodysplastic syndrome: a systematic review of hypomethylating agents trials. Clin Epigenetics. 2016;8:68.

    Article  Google Scholar 

  20. 20.

    Gore SD, Baylin S, Sugar E, Carraway H, Miller CB, Carducci M, et al. Combined DNA methyltransferase and histone deacetylase inhibition in the treatment of myeloid neoplasms. Cancer Res. 2006;66:6361–9.

    CAS  Article  Google Scholar 

  21. 21.

    Cowan LA, Talwar S, Yang AS. Will DNA methylation inhibitors work in solid tumors? A review of the clinical experience with azacitidine and decitabine in solid tumors. Epigenomics. 2010;2:71–86.

    CAS  Article  Google Scholar 

  22. 22.

    Schneider BJ, Shah MA, Klute K, Ocean A, Popa E, Altorki N, et al. Phase I study of epigenetic priming with azacitidine prior to standard neoadjuvant chemotherapy for patients with resectable gastric and esophageal adenocarcinoma: evidence of tumor hypomethylation as an indicator of major histopathologic response. Clin Cancer Res. 2017;23:2673–80.

    CAS  Article  Google Scholar 

  23. 23.

    Juergens RA, Wrangle J, Vendetti FP, Murphy SC, Zhao M, Coleman B, et al. Combination epigenetic therapy has efficacy in patients with refractory advanced non-small cell lung cancer. Cancer Discov. 2011;1:598–607.

    CAS  Article  Google Scholar 

  24. 24.

    Fang F, Munck J, Tang J, Taverna P, Wang Y, Miller DF, et al. The novel, small-molecule DNA methylation inhibitor SGI-110 as an ovarian cancer chemosensitizer. Clin Cancer Res. 2014;20:6504–16.

    CAS  Article  Google Scholar 

  25. 25.

    Welch JS, Petti AA, Miller CA, Fronick CC, O’Laughlin M, Fulton RS, et al. TP53 and decitabine in acute myeloid leukemia and myelodysplastic syndromes. N Engl J Med. 2016;375:2023–36.

    CAS  Article  Google Scholar 

  26. 26.

    Zouridis H, Deng N, Ivanova T, Zhu Y, Wong B, Huang D, et al. Methylation subtypes and large-scale epigenetic alterations in gastric cancer. Sci Transl Med. 2012;4:156ra140.

    Article  Google Scholar 

  27. 27.

    Stewart ML, Tamayo P, Wilson AJ, Wang S, Chang YM, Kim JW, et al. KRAS genomic status predicts the sensitivity of ovarian cancer cells to decitabine. Cancer Res. 2015;75:2897–906.

    CAS  Article  Google Scholar 

  28. 28.

    Uemura N, Okamoto S, Yamamoto S, Matsumura N, Yamaguchi S, Yamakido M, et al. Helicobacter pylori infection and the development of gastric cancer. N Engl J Med. 2001;345:784–9.

    CAS  Article  Google Scholar 

  29. 29.

    Ajani JA, Lee J, Sano T, Janjigian YY, Fan D, Song S. Gastric adenocarcinoma. Nat Rev Dis Prim. 2017;3:17036.

    Article  Google Scholar 

  30. 30.

    Cui Y, Hausheer F, Beaty R, Zahnow C, Issa JP, Bunz F, et al. A recombinant reporter system for monitoring reactivation of an endogenously DNA hypermethylated gene. Cancer Res. 2014;74:3834–43.

    CAS  Article  Google Scholar 

  31. 31.

    Chuang JC, Warner SL, Vollmer D, Vankayalapati H, Redkar S, Bearss DJ, et al. S110, a 5-Aza-2′-deoxycytidine-containing dinucleotide, is an effective DNA methylation inhibitor in vivo and can reduce tumor growth. Mol Cancer Ther. 2010;9:1443–50.

    CAS  Article  Google Scholar 

  32. 32.

    Hironaka S, Sugimoto N, Yamaguchi K, Moriwaki T, Komatsu Y, Nishina T, et al. S-1 plus leucovorin versus S-1 plus leucovorin and oxaliplatin versus S-1 plus cisplatin in patients with advanced gastric cancer: a randomised, multicentre, open-label, phase 2 trial. Lancet Oncol. 2016;17:99–108.

    CAS  Article  Google Scholar 

  33. 33.

    Cascinu S, Labianca R, Alessandroni P, Marcellini M, Silva RR, Pancera G, et al. Intensive weekly chemotherapy for advanced gastric cancer using fluorouracil, cisplatin, epi-doxorubicin, 6S-leucovorin, glutathione, and filgrastim: a report from the Italian Group for the Study of Digestive Tract Cancer. J Clin Oncol. 1997;15:3313–9.

    CAS  Article  Google Scholar 

  34. 34.

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

    CAS  Article  Google Scholar 

  35. 35.

    Liu B, Sun L, Liu Q, Gong C, Yao Y, Lv X, et al. A cytoplasmic NF-kappaB interacting long noncoding RNA blocks IkappaB phosphorylation and suppresses breast cancer metastasis. Cancer Cell. 2015;27:370–81.

    CAS  Article  Google Scholar 

  36. 36.

    Katsushima K, Natsume A, Ohka F, Shinjo K, Hatanaka A, Ichimura N, et al. Targeting the Notch-regulated non-coding RNA TUG1 for glioma treatment. Nat Commun. 2016;7:13616.

    Article  Google Scholar 

  37. 37.

    Garneau D, Revil T, Fisette JF, Chabot B. Heterogeneous nuclear ribonucleoprotein F/H proteins modulate the alternative splicing of the apoptotic mediator Bcl-x. J Biol Chem. 2005;280:22641–50.

    CAS  Article  Google Scholar 

  38. 38.

    Chandler DS, Singh RK, Caldwell LC, Bitler JL, Lozano G. Genotoxic stress induces coordinately regulated alternative splicing of the p53 modulators MDM2 and MDM4. Cancer Res. 2006;66:9502–8.

    CAS  Article  Google Scholar 

  39. 39.

    Mills JD, Kavanagh T, Kim WS, Chen BJ, Kawahara Y, Halliday GM, et al. Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe. PLoS ONE. 2013;8:e78480.

    CAS  Article  Google Scholar 

  40. 40.

    Lu M, Tian H, Cao YX, He X, Chen L, Song X, et al. Downregulation of miR-320a/383-sponge-like long non-coding RNA NLC1-C (narcolepsy candidate-region 1 genes) is associated with male infertility and promotes testicular embryonal carcinoma cell proliferation. Cell Death Dis. 2015;6:e1960.

    CAS  Article  Google Scholar 

  41. 41.

    Lu M, Ding K, Zhang G, Yin M, Yao G, Tian H, et al. MicroRNA-320a sensitizes tamoxifen-resistant breast cancer cells to tamoxifen by targeting ARPP-19 and ERRgamma. Sci Rep. 2015;5:8735.

    CAS  Article  Google Scholar 

  42. 42.

    He DX, Gu XT, Jiang L, Jin J, Ma X. A methylation-based regulatory network for microRNA 320a in chemoresistant breast cancer. Mol Pharmacol. 2014;86:536–47.

    Article  Google Scholar 

  43. 43.

    Gao X, Shen K, Wang C, Ling J, Wang H, Fang Y, et al. MiR-320a downregulation is associated with imatinib resistance in gastrointestinal stromal tumors. Acta Biochim Biophys Sin (Shanghai). 2014;46:72–75.

    CAS  Article  Google Scholar 

  44. 44.

    Piipponen M, Nissinen L, Farshchian M, Riihila P, Kivisaari A, Kallajoki M, et al. Long noncoding RNA PICSAR promotes growth of cutaneous squamous cell carcinoma by regulating ERK1/2 Activity. J Invest Dermatol. 2016;136:1701–10.

    CAS  Article  Google Scholar 

  45. 45.

    Greenberg PL, Attar E, Bennett JM, Bloomfield CD, De Castro CM, Deeg HJ, et al. NCCN Clinical Practice Guidelines in Oncology: myelodysplastic syndromes. J Natl Compr Canc Netw. 2011;9:30–56.

    Article  Google Scholar 

  46. 46.

    Magklara A, Scorilas A, Katsaros D, Massobrio M, Yousef GM, Fracchioli S, et al. The human KLK8 (neuropsin/ovasin) gene: identification of two novel splice variants and its prognostic value in ovarian cancer. Clin Cancer Res. 2001;7:806–11.

    CAS  PubMed  Google Scholar 

  47. 47.

    Man CH, Lam SS, Sun MK, Chow HC, Gill H, Kwong YL, et al. A novel tescalcin-sodium/hydrogen exchange axis underlying sorafenib resistance in FLT3-ITD + AML. Blood. 2014;123:2530–9.

    CAS  Article  Google Scholar 

  48. 48.

    Lustig B, Jerchow B, Sachs M, Weiler S, Pietsch T, Karsten U, et al. Negative feedback loop of Wnt signaling through upregulation of conductin/axin2 in colorectal and liver tumors. Mol Cell Biol. 2002;22:1184–93.

    CAS  Article  Google Scholar 

  49. 49.

    Okochi-Takada E, Hattori N, Tsukamoto T, Miyamoto K, Ando T, Ito S, et al. ANGPTL4 is a secreted tumor suppressor that inhibits angiogenesis. Oncogene. 2014;33:2273–8.

    CAS  Article  Google Scholar 

  50. 50.

    Kim JG, Takeshima H, Niwa T, Rehnberg E, Shigematsu Y, Yoda Y, et al. Comprehensive DNA methylation and extensive mutation analyses reveal an association between the CpG island methylator phenotype and oncogenic mutations in gastric cancers. Cancer Lett. 2013;330:33–40.

    CAS  Article  Google Scholar 

  51. 51.

    Zong L, Hattori N, Yoda Y, Yamashita S, Takeshima H, Takahashi T, et al. Establishment of a DNA methylation marker to evaluate cancer cell fraction in gastric cancer. Gastric Cancer. 2016;19:361–9.

    CAS  Article  Google Scholar 

  52. 52.

    Asada K, Ando T, Niwa T, Nanjo S, Watanabe N, Okochi-Takada E, et al. FHL1 on chromosome X is a single-hit gastrointestinal tumor-suppressor gene and contributes to the formation of an epigenetic field defect. Oncogene. 2013;32:2140–9.

    CAS  Article  Google Scholar 

Download references


This study was supported by AMED under Grant Number JP18ck0106421 to Toshikazu Ushijima and JSPS KAKENHI under Grant Number JP18H02704 to Toshikazu Ushijima.

Author information




T.U., L.Z. and N.H. designed the study; L.Z., N.H., Y.Y. and K.K. performed most of the experiments; A.M., K.K. and N.H. performed in vivo experiments; L.Z. and N.H. wrote the manuscript; T.U., N.H., Y.Y. and Y.S. revised the manuscript; and all authors read and approved the manuscript.

Corresponding author

Correspondence to Toshikazu Ushijima.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

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

Verify currency and authenticity via CrossMark

Cite this article

Zong, L., Hattori, N., Yasukawa, Y. et al. LINC00162 confers sensitivity to 5-Aza-2′-deoxycytidine via modulation of an RNA splicing protein, HNRNPH1. Oncogene 38, 5281–5293 (2019).

Download citation

Further reading


Quick links