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  • Original Article
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DNA methylation in small cell lung cancer defines distinct disease subtypes and correlates with high expression of EZH2

Abstract

Small cell lung cancer (SCLC) is an aggressive malignancy characterized by early metastasis, rapid development of resistance to chemotherapy and genetic instability. This study profiles DNA methylation in SCLC, patient-derived xenografts (PDX) and cell lines at single-nucleotide resolution. DNA methylation patterns of primary samples are distinct from those of cell lines, whereas PDX maintain a pattern closely consistent with primary samples. Clustering of DNA methylation and gene expression of primary SCLC revealed distinct disease subtypes among histologically indistinguishable primary patient samples with similar genetic alterations. SCLC is notable for dense clustering of high-level methylation in discrete promoter CpG islands, in a pattern clearly distinct from other lung cancers and strongly correlated with high expression of the E2F target and histone methyltransferase gene EZH2. Pharmacologic inhibition of EZH2 in a SCLC PDX markedly inhibited tumor growth.

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References

  1. Siegel R, Naishadham D, Jemal A . Cancer statistics 2012 CA Cancer J Clin 2012; 62: 10–29.

    Article  Google Scholar 

  2. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D . Global cancer statistics. CA Cancer J Clin 2011; 61: 69–90.

    Article  Google Scholar 

  3. Wistuba II, Gazdar AF, Minna JD . Molecular genetics of small cell lung carcinoma. Semin Oncol 2001; 28: 3–13.

    Article  CAS  Google Scholar 

  4. Oze I, Hotta K, Kiura K, Ochi N, Takigawa N, Fujiwara Y et al. Twenty-seven years of phase III trials for patients with extensive disease small-cell lung cancer: disappointing results. PLoS One 2009; 4: e7835.

    Article  Google Scholar 

  5. Madrigal PA, Manga GP, Palomero I, Gomez RG . VP16-213 combined with cis-platinum (CDDP) in the treatment of small cell carcinoma of the lung (SCLC). Cancer Chemother Pharmacol 1982; 7: 203–204.

    Article  CAS  Google Scholar 

  6. Lara PN Jr., Natale R, Crowley J, Lenz HJ, Redman MW, Carleton JE et al. Phase III trial of irinotecan/cisplatin compared with etoposide/cisplatin in extensive-stage small-cell lung cancer: clinical and pharmacogenomic results from SWOG S0124. J Clin Oncol 2009; 27: 2530–2535.

    Article  CAS  Google Scholar 

  7. Rudin CM, Durinck S, Stawiski EW, Poirier JT, Modrusan Z, Shames DS et al. Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet 2012; 44: 1111–1116.

    Article  CAS  Google Scholar 

  8. Peifer M, Fernandez-Cuesta L, Sos ML, George J, Seidel D, Kasper LH et al. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet 2012; 44: 1104–1110.

    Article  CAS  Google Scholar 

  9. Clinical Lung Cancer Genome Project, Network Genomic Medicine. A genomics-based classification of human lung tumors. Sci Transl Med 2013; 5: 209ra153.

    Google Scholar 

  10. Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012; 489: 519–525.

    Article  Google Scholar 

  11. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012; 487: 330–337.

    Article  Google Scholar 

  12. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 2012; 490: 61–70.

    Article  Google Scholar 

  13. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008; 455: 1061–1068.

    Article  Google Scholar 

  14. Kalari S, Jung M, Kernstine KH, Takahashi T, Pfeifer GP . The DNA methylation landscape of small cell lung cancer suggests a differentiation defect of neuroendocrine cells. Oncogene 2013; 32: 3559–3568.

    Article  CAS  Google Scholar 

  15. Rauch T, Pfeifer GP . Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 2005; 85: 1172–1180.

    Article  CAS  Google Scholar 

  16. Hann CL, Rudin CM . Fast, hungry and unstable: finding the Achilles' heel of small-cell lung cancer. Trends Mol Med 2007; 13: 150–157.

    Article  CAS  Google Scholar 

  17. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011; 43: 768–775.

    Article  CAS  Google Scholar 

  18. Poirier JT, Dobromilskaya I, Moriarty WF, Peacock CD, Hann CL, Rudin CM . Selective tropism of Seneca Valley virus for variant subtype small cell lung cancer. J Natl Cancer Instit 2013; 105: 1059–1065.

    Article  CAS  Google Scholar 

  19. Carney DN, Gazdar AF, Bepler G, Guccion JG, Marangos PJ, Moody TW et al. Establishment and identification of small cell lung cancer cell lines having classic and variant features. Cancer Res 1985; 45: 2913–2923.

    CAS  Google Scholar 

  20. Daniel VC, Marchionni L, Hierman JS, Rhodes JT, Devereux WL, Rudin CM et al. A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. Cancer Res 2009; 69: 3364–3373.

    Article  CAS  Google Scholar 

  21. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC et al. Multiple-laboratory comparison of microarray platforms. Nat Methods 2005; 2: 345–350.

    Article  CAS  Google Scholar 

  22. Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 2012; 44: 40–46.

    Article  CAS  Google Scholar 

  23. Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP et al. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol 2012; 41: 200–209.

    Article  Google Scholar 

  24. Gardner EE, Connis N, Poirier JT, Cope L, Dobromilskaya I, Gallia GL et al. Rapamycin rescues ABT-737 efficacy in small cell lung cancer. Cancer Res 2014; 74: 2846–2856.

    Article  CAS  Google Scholar 

  25. Smith LT, Lin M, Brena RM, Lang JC, Schuller DE, Otterson GA et al. Epigenetic regulation of the tumor suppressor gene TCF21 on 6q23-q24 in lung and head and neck cancer. Proc Natl Acad Sci USA 2006; 103: 982–987.

    Article  CAS  Google Scholar 

  26. Wilkerson MD, Yin X, Hoadley KA, Liu Y, Hayward MC, Cabanski CR et al. Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types. Clin Cancer Res 2010; 16: 4864–4875.

    Article  CAS  Google Scholar 

  27. Mack SC, Witt H, Piro RM, Gu L, Zuyderduyn S, Stutz AM et al. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature 2014; 506: 445–450.

    Article  CAS  Google Scholar 

  28. 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: 156ra40.

    Article  Google Scholar 

  29. Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 2010; 17: 510–522.

    Article  CAS  Google Scholar 

  30. Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, Faasse MA et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 2006; 38: 787–793.

    Article  CAS  Google Scholar 

  31. Bady P, Sciuscio D, Diserens AC, Bloch J, van den Bent MJ, Marosi C et al. MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status. Acta Neuropath 2012; 124: 547–560.

    Article  CAS  Google Scholar 

  32. Chang CJ, Hung MC . The role of EZH2 in tumour progression. Brit J Cancer 2012; 106: 243–247.

    Article  CAS  Google Scholar 

  33. Bracken AP, Pasini D, Capra M, Prosperini E, Colli E, Helin K . EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J 2003; 22: 5323–5335.

    Article  CAS  Google Scholar 

  34. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW . Cancer genome landscapes. Science 2013; 339: 1546–1558.

    Article  CAS  Google Scholar 

  35. Byers LA, Wang J, Nilsson MB, Fujimoto J, Saintigny P, Yordy J et al. Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov 2012; 2: 798–811.

    Article  CAS  Google Scholar 

  36. Ziller MJ, Gu H, Muller F, Donaghey J, Tsai LT, Kohlbacher O et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 2013; 500: 477–481.

    Article  CAS  Google Scholar 

  37. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res 2013; 23: 555–567.

    Article  CAS  Google Scholar 

  38. Wilkerson MD, Yin X, Walter V, Zhao N, Cabanski CR, Hayward MC et al. Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation. PLoS One 2012; 7: e36530.

    Article  CAS  Google Scholar 

  39. Meuwissen R, Linn SC, Linnoila RI, Zevenhoven J, Mooi WJ, Berns A . Induction of small cell lung cancer by somatic inactivation of both Trp53 and Rb1 in a conditional mouse model. Cancer Cell 2003; 4: 181–189.

    Article  CAS  Google Scholar 

  40. Wee ZN, Li Z, Lee PL, Lee ST, Lim YP, Yu Q . EZH2-mediated inactivation of IFN-gamma-JAK-STAT1 signaling is an effective therapeutic target in MYC-driven prostate cancer. Cell Rep 2014; 8: 204–216.

    Article  CAS  Google Scholar 

  41. Kim W, Bird GH, Neff T, Guo G, Kerenyi MA, Walensky LD et al. Targeted disruption of the EZH2-EED complex inhibits EZH2-dependent cancer. Nat Chem Biol 2013; 9: 643–650.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Inna Kodos in the Sloan Kettering Antitumor Assessment Core for her technical expertise. We are grateful to all members of the Rudin and Hann labs for thoughtful discussions. SU2C, P30 CA008748 gave financial support.

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Correspondence to C M Rudin.

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CMR has been a paid consultant regarding cancer drug development for AbbVie, Aveo, Celgene, GlaxoSmithKline and Merck. The remaining authors declare no conflict of interest.

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Supplementary Information accompanies this paper on the Oncogene website

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Poirier, J., Gardner, E., Connis, N. et al. DNA methylation in small cell lung cancer defines distinct disease subtypes and correlates with high expression of EZH2. Oncogene 34, 5869–5878 (2015). https://doi.org/10.1038/onc.2015.38

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