Breast Cancer Research and Treatment

, Volume 136, Issue 3, pp 875–883 | Cite as

Association of large noncoding RNA HOTAIR expression and its downstream intergenic CpG island methylation with survival in breast cancer

  • Lingeng Lu
  • Guangjian Zhu
  • Chong Zhang
  • Qian Deng
  • Dionyssios Katsaros
  • Susan T. Mayne
  • Harvey A. Risch
  • Lina Mu
  • Emilie Marion Canuto
  • Gianluca Gregori
  • Chiara Benedetto
  • Herbert Yu


Large noncoding RNA HOTAIR, transcribed from the antisense strand of HOXC12, interacts with Polycomb Repressive Complex 2 (PRC2) in the regulation of gene activities. Recent work suggests that it may have effects on breast cancer progression and survival. We evaluated HOTAIR expression and the methylation status of its downstream intergenic CpG island in primary breast cancers, and examined associations of these factors with clinical and pathologic features and patient survival. HOTAIR expression and DNA methylation were analyzed in tissue from 348 primary breast cancers with quantitative RT-PCR and methylation-specific PCR, respectively. HOTAIR expression and methylation varied widely in the tissues. A positive correlation was found between DNA methylation and HOTAIR expression. Methylation was associated with unfavorable disease characteristics, whereas no significant associations were found between HOTAIR expression and clinical or pathologic features. In multivariate, but not in univariate, Cox proportional hazard regression models, patients with high HOTAIR expression had lower risks of relapse and mortality than those with low HOTAIR expression. These findings suggest that the intergenic DNA methylation may have important biologic relevance in regulating HOTAIR expression, and that HOTAIR expression may not be an independent prognostic marker in breast cancer, but needs further validation in independent studies.


Large non-coding RNA DNA methylation Gene expression Breast cancer Prognosis 


Conflict of interest

The authors declare that there are no conflicts of interest.


  1. 1.
    Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323PubMedCrossRefGoogle Scholar
  2. 2.
    Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A et al (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106:11667–11672PubMedCrossRefGoogle Scholar
  3. 3.
    Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464:1071–1076PubMedCrossRefGoogle Scholar
  4. 4.
    Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS et al (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4:e1000242PubMedCrossRefGoogle Scholar
  5. 5.
    Bracken AP, Dietrich N, Pasini D, Hansen KH, Helin K (2006) Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev 20:1123–1136PubMedCrossRefGoogle Scholar
  6. 6.
    Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329:689–693PubMedCrossRefGoogle Scholar
  7. 7.
    Medvedeva YA, Fridman MV, Oparina NJ, Malko DB, Ermakova EO, Kulakovskiy IV, Heinzel A, Makeev VJ (2010) Intergenic, gene terminal, and intragenic CpG islands in the human genome. BMC Genomics 11:48PubMedCrossRefGoogle Scholar
  8. 8.
    Lujambio A, Portela A, Liz J, Melo SA, Rossi S, Spizzo R, Croce CM, Calin GA, Esteller M (2010) CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer. Oncogene 29:6390–6401PubMedCrossRefGoogle Scholar
  9. 9.
    Choi JK, Bae JB, Lyu J, Kim TY, Kim YJ (2009) Nucleosome deposition and DNA methylation at coding region boundaries. Genome Biol 10:R89PubMedCrossRefGoogle Scholar
  10. 10.
    Kornblihtt AR (2006) Chromatin, transcript elongation and alternative splicing. Nat Struct Mol Biol 13:5–7PubMedCrossRefGoogle Scholar
  11. 11.
    Sims RJ 3rd, Reinberg D (2009) Processing the H3K36me3 signature. Nat Genet 41:270–271PubMedCrossRefGoogle Scholar
  12. 12.
    Lu L, Katsaros D, Wiley A, Rigault de la Longrais IA, Risch HA, Puopolo M, Yu H (2006) The relationship of insulin-like growth factor-II, insulin-like growth factor binding protein-3, and estrogen receptor-alpha expression to disease progression in epithelial ovarian cancer. Clin Cancer Res 12:1208–1214PubMedCrossRefGoogle Scholar
  13. 13.
    Mu L, Katsaros D, Wiley A, Lu L, de la Longrais IA, Smith S, Khubchandani S, Sochirca O, Arisio R, Yu H (2009) Peptide concentrations and mRNA expression of IGF-I, IGF-II and IGFBP-3 in breast cancer and their associations with disease characteristics. Breast Cancer Res Treat 115:151–162PubMedCrossRefGoogle Scholar
  14. 14.
    Jepsen K, Solum D, Zhou T, McEvilly RJ, Kim HJ, Glass CK, Hermanson O, Rosenfeld MG (2007) SMRT-mediated repression of an H3K27 demethylase in progression from neural stem cell to neuron. Nature 450:415–419PubMedCrossRefGoogle Scholar
  15. 15.
    Mu L, Tuck D, Katsaros D, Lu L, Schulz V, Perincheri S, Menato G, Scarampi L, Harris L, Yu H (2012) Favorable outcome associated with an IGF-1 ligand signature in breast cancer. Breast Cancer Res Treat 133:321–331PubMedCrossRefGoogle Scholar
  16. 16.
    Mansour AA, Gafni O, Weinberger L, Zviran A, Ayyash M, Rais Y, Krupalnik V, Zerbib M, Amann-Zalcenstein D, Maza I et al (2012) The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 488:409–413PubMedCrossRefGoogle Scholar
  17. 17.
    Welstead GG, Creyghton MP, Bilodeau S, Cheng AW, Markoulaki S, Young RA, Jaenisch R (2012) X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner. Proc Natl Acad Sci U S A 109:13004–13009PubMedCrossRefGoogle Scholar
  18. 18.
    Kim K, Jutooru I, Chadalapaka G, Johnson G, Frank J, Burghardt R, Kim S, Safe S (2012) HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene. doi: 10.1038/onc.2012.193.
  19. 19.
    Wu H, Coskun V, Tao J, Xie W, Ge W, Yoshikawa K, Li E, Zhang Y, Sun YE (2010) Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329:444–448PubMedCrossRefGoogle Scholar
  20. 20.
    Vire E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden JM et al (2006) The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439:871–874PubMedCrossRefGoogle Scholar
  21. 21.
    Rush M, Appanah R, Lee S, Lam LL, Goyal P, Lorincz MC (2009) Targeting of EZH2 to a defined genomic site is sufficient for recruitment of Dnmt3a but not de novo DNA methylation. Epigenetics 4:404–414PubMedCrossRefGoogle Scholar
  22. 22.
    Lim DA, Huang YC, Swigut T, Mirick AL, Garcia-Verdugo JM, Wysocka J, Ernst P, Alvarez-Buylla A (2009) Chromatin remodelling factor Mll1 is essential for neurogenesis from postnatal neural stem cells. Nature 458:529–533PubMedCrossRefGoogle Scholar
  23. 23.
    Euhus DM, Bu D, Milchgrub S, Xie XJ, Bian A, Leitch AM, Lewis CM (2008) DNA methylation in benign breast epithelium in relation to age and breast cancer risk. Cancer Epidemiol Biomarkers Prev 17:1051–1059PubMedCrossRefGoogle Scholar
  24. 24.
    Christensen BC, Kelsey KT, Zheng S, Houseman EA, Marsit CJ, Wrensch MR, Wiemels JL, Nelson HH, Karagas MR, Kushi LH et al (2010) Breast cancer DNA methylation profiles are associated with tumor size and alcohol and folate intake. PLoS Genet 6:e1001043PubMedCrossRefGoogle Scholar
  25. 25.
    Wang S, Dorsey TH, Terunuma A, Kittles RA, Ambs S, Kwabi-Addo B (2012) Relationship between tumor DNA methylation status and patient characteristics in African-American and European-American women with breast cancer. PLoS ONE 7:e37928PubMedCrossRefGoogle Scholar
  26. 26.
    Boks MP, Derks EM, Weisenberger DJ, Strengman E, Janson E, Sommer IE, Kahn RS, Ophoff RA (2009) The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS ONE 4:e6767PubMedCrossRefGoogle Scholar
  27. 27.
    He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XS (2012) Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res 22:1015–1025PubMedCrossRefGoogle Scholar
  28. 28.
    Zubko E, Kunova A, Meyer P (2011) Sense and antisense transcripts of convergent gene pairs in Arabidopsis thaliana can share a common polyadenylation region. PLoS ONE 6:e16769PubMedCrossRefGoogle Scholar
  29. 29.
    Greger IH, Proudfoot NJ (1998) Poly(A) signals control both transcriptional termination and initiation between the tandem GAL10 and GAL7 genes of Saccharomyces cerevisiae. EMBO J 17:4771–4779PubMedCrossRefGoogle Scholar
  30. 30.
    Kim SJ, Martinson HG (2003) Poly(A)-dependent transcription termination: continued communication of the poly(A) signal with the polymerase is required long after extrusion in vivo. J Biol Chem 278:41691–41701PubMedCrossRefGoogle Scholar
  31. 31.
    Herold M, Bartkuhn M, Renkawitz R (2012) CTCF: insights into insulator function during development. Development 139:1045–1057PubMedCrossRefGoogle Scholar
  32. 32.
    Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB et al (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766–770PubMedGoogle Scholar
  33. 33.
    Lorincz MC, Dickerson DR, Schmitt M, Groudine M (2004) Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol 11:1068–1075PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Lingeng Lu
    • 1
  • Guangjian Zhu
    • 1
    • 2
  • Chong Zhang
    • 1
    • 3
  • Qian Deng
    • 1
    • 4
  • Dionyssios Katsaros
    • 5
  • Susan T. Mayne
    • 1
  • Harvey A. Risch
    • 1
  • Lina Mu
    • 6
  • Emilie Marion Canuto
    • 5
  • Gianluca Gregori
    • 5
  • Chiara Benedetto
    • 5
  • Herbert Yu
    • 1
    • 7
  1. 1.Department of Chronic Disease Epidemiology, Yale Cancer CenterYale School of Public HealthNew HavenUSA
  2. 2.Gansu Provincial Academy of Medical ScienceGansu Provincial Tumor HospitalLanzhouChina
  3. 3.Gansu Provincial Hospital for the Protection of Mother and Baby’s HealthLanzhouChina
  4. 4.National Center for Chronic and Non-communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
  5. 5.Department of Gynecologic OncologyAzienda Ospedaliera OIRM-S.ANNA and University of TorinoTurinItaly
  6. 6.Department of Social and Preventive MedicineUniversity at Buffalo, The State University of New YorkBuffaloUSA
  7. 7.Epidemiology ProgramUniversity of Hawaii Cancer CenterHonoluluUSA

Personalised recommendations