Skip to main content

DNA and Histone Methylation in Lung Cancer

  • Chapter
  • First Online:
DNA and Histone Methylation as Cancer Targets

Part of the book series: Cancer Drug Discovery and Development ((CDD&D))

Abstract

Oncogenesis is driven by the accumulation of genetic and epigenetic alterations that result in dysregulation of key oncogenes, tumor suppressor genes, and DNA repair/housekeeping genes. One of the major clinical needs is the discovery and clinical validation of new molecular biomarkers using non-or minimally invasive procedures to assist early diagnosis, prognosis and prediction of response to treatment. Histone methylation has profound effects on nuclear functions such as transcriptional regulation, maintenance of genome integrity and epigenetic inheritance. On the other hand, aberrant DNA methylation can be detected in several biological fluids of patients and could be served as a potential tumor biomarker. In the present chapter we describe latest developments on histone and DNA methylation based biomarkers in Lung cancer.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Abu Khaled M, Watkins CL, Krumdieck CL (1986) Inactivation of B12 and folate coenzymes by butyl nitrite as observed by NMR: implications on one-carbon transfer mechanism. Biochem Biophys Res Commun 135:201–207

    Article  CAS  PubMed  Google Scholar 

  2. Altenberger C, Heller C, Ziegler B, Tomasich E, Marhold M, Topakian T et al (2017) SPAG6 and L1TD1 are transcriptionally regulated by DNA methylation in non-small cell lung cancers. Mol Cancer 16:1

    Article  PubMed  PubMed Central  Google Scholar 

  3. Andujar P, Wang J, Descatha A, Galateau-Sallé F, Abd-Alsamad I, Billon-Galland MA et al (2010) p16INK4A inactivation mechanisms in non-small-cell patients with lung cancer occupationally exposed to asbestos. Lung Cancer 67:23–30

    Article  PubMed  Google Scholar 

  4. Anisowicz A, Huang H, Braunschweiger KI, Liu Z, Giese H, Wang H et al (2008) A highthroughput and sensitive method to measure global DNA methylation: application in lung cancer. BMC Cancer 8:222

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Ansari J, Shackelford RE, El-Osta H (2016) Epigenetics in non-small cell lung cancer: from basics to therapeutics. Transl Lung Cancer Res 5(2):155–171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Bailey-Wilson JE, Amos CI, Pinney SM, Petersen GM, de Andrade M, Wiest JS et al (2004) A major lung cancer susceptibility locus maps to chromosome 6q23-25. Am J Hum Genet 75:460–474

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Baldwin DR, Duffy SW, Wald NJ, Page R, Hansell DM, Field JK (2011) UK lung screen (UKLS) nodule management protocol: modelling of a single screen randomised controlled trial of low-dose CT screening for lung cancer. Thorax 66(4):308–313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Balgkouranidou I, Liloglou T, Lianidou ES (2013) Lung cancer epigenetics: emerging biomarkers. Biomark Med 7(1):49–58

    Article  CAS  PubMed  Google Scholar 

  9. Balgkouranidou I, Chimonidou M, Milaki G, Tsarouxa EG, Kakolyris S, Welch DR et al (2014) Breast cancer metastasis suppressor-1 promoter methylation in cell-free DNA provides prognostic information in non-small cell lung cancer. Br J Cancer 110:2054–2062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Balgkouranidou I, Chimonidou M, Milaki G, Tsaroucha E, Kakolyris S, Georgoulias V et al (2016) SOX17 promoter methylation in plasma circulating tumor DNA of patients with non-small cell lung cancer. Clin Chem Lab Med 54:1385–1393

    Article  CAS  PubMed  Google Scholar 

  11. Balkwill F, Coussens LM (2004) Cancer: an inflammatory link. Nature 431:405–406

    Article  CAS  PubMed  Google Scholar 

  12. Bardelli A, Pantel K (2017) Liquid biopsies, what we do not know (yet). Cancer Cell 31(2):172–179

    Article  CAS  PubMed  Google Scholar 

  13. Barlesi F, Giaccone G, Gallegos-Ruiz MI, Loundou A, Span SW, Lefesvre P et al (2007) Global histone modifications predict prognosis of resected non small-cell lung cancer. J Clin Oncol 25(28):4358–4364

    Article  PubMed  Google Scholar 

  14. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837

    Article  CAS  PubMed  Google Scholar 

  15. Bartling B, Hofmann HS, Boettger T, Hansen G, Burdach S, Silber RE et al (2005) Comparative application of antibody and gene array for expression profiling in human squamous cell lung carcinoma. Lung Cancer 49:145–154

    Article  PubMed  Google Scholar 

  16. Bearzatto A, Conte D, Frattini M, Zaffaroni N, Andriani F, Balestra D et al (2002) p16(INK4A) Hypermethylation detected by fluorescent methylation-specific PCR in plasmas from non-small cell lung cancer. Clin Cancer Res 8(12):3782–3787

    CAS  PubMed  Google Scholar 

  17. Beck CR, Garcia-Perez JL, Badge RM, Moran JV (2011) LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet 12:187–215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Belinsky SA (2005) Silencing of genes by promoter hypermethylation: key event in rodent and human lung cancer. Carcinogenesis 26:1481–1487

    Article  CAS  PubMed  Google Scholar 

  19. Belinsky SA (2015) Unmasking the lung cancer epigenome. Annu Rev Physiol 77:453–474

    Article  CAS  PubMed  Google Scholar 

  20. Belinsky SA, Nikula KJ, Palmisano WA, Michels R, Saccomanno G, Gabrielson E et al (1998) Aberrant methylation of p16(INK4a) is an early event in lung cancer and a potential biomarker for early diagnosis. Proc Natl Acad Sci U S A 95:11891–11896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Belinsky SA, Klinge DM, Dekker JD, Smith MW, Bocklage TJ, Gilliland FD et al (2005) Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clin Cancer Res 11:6505–6511

    Article  CAS  PubMed  Google Scholar 

  22. Belinsky SA, Liechty KC, Gentry FD, Wolf HJ, Rogers J, Vu K et al (2006) Promoter hypermethylation of multiple genes in sputum precedes lung cancer incidence in a high-risk cohort. Cancer Res 66:3338–3344

    Article  CAS  PubMed  Google Scholar 

  23. Belinsky SA, Grimes MJ, Casas E, Stidley CA, Franklin WA, Bocklage TJ et al (2007) Predicting gene promoter methylation in non-small-cell lung cancer by evaluating sputum and serum. Br J Cancer 96(8):1278–1283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Berger AH, Knudson AG, Pandolfi PP (2011) A continuum model for tumour suppression. Nature 476:163–169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Blount BC, Mack MM, Wehr CM, MacGregor JT, Hiatt RA, Wang G et al (1997) Folate deficiency causes uracil misincorporation into human DNA and chromosome breakage: implications for cancer and neuronal damage. Proc Natl Acad Sci U S A 94:3290–3295

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Brabender J, Usadel H, Danenberg KD, Metzger R, Schneider PM, Lord RV et al (2001) Adenomatous polyposis coli gene promoter hypermethylation in non-small cell lung cancer is associated with survival. Oncogene 20:3528–3532

    Article  CAS  PubMed  Google Scholar 

  27. Brock MV, Hooker CM, Ota-Machida E, Han Y, Guo M, Ames S et al (2008) DNA methylation markers and early recurrence in stage I lung cancer. N Engl J Med 358:1118–1128

    Article  CAS  PubMed  Google Scholar 

  28. Brzezianska E, Dutkowska A, Antczak A (2013) The significance of epigenetic alterations in lung carcinogenesis. Mol Biol Rep 40:309–325

    Article  CAS  PubMed  Google Scholar 

  29. Chen H, Suzuki M, Nakamura Y, Ohira M, Ando S, Iida T et al (2005) Aberrant methylation of FBN2 in human non-small cell lung cancer. Lung Cancer 50:43–49

    Article  PubMed  Google Scholar 

  30. Cheng J, Blum R, Bowman C, Hu D, Shilatifard A, Shen S et al (2014) A role for H3K4 monomethylation in gene repression and partitioning of chromatin readers. Mol Cell 53:979–992

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Chi P, Allis CD, Wang GG (2010) Covalent histone modifications – miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 10:457–469

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Christman JK (2002) 5-Azacytidine and 5-aza-2′-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy. Oncogene 21:5483–5495

    Article  CAS  PubMed  Google Scholar 

  33. Cirincione R, Lintas C, Conte D, Mariani L, Roz L, Vignola AM et al (2006) Methylation profile in tumor and sputum samples of lung cancer patients detected by spiral computed tomography: a nested case–control study. Int J Cancer 118(5):1248–1253

    Article  CAS  PubMed  Google Scholar 

  34. Damiani LA, Yingling CM, Leng S, Romo PE, Nakamura J, Belinsky SA (2008) Carcinogeninduced gene promoter hypermethylation is mediated by DNMT1 and causal for transformation of immortalized bronchial epithelial cells. Cancer Res 68:9005–9014

    Article  CAS  PubMed  Google Scholar 

  35. Daskalos A, Logotheti S, Markopoulou S, Xinarianos G, Gosney JR, Kastania AN et al (2011) Global DNA hypomethylation-induced deltaNp73 transcriptional activation in non-small cell lung cancer. Cancer Lett 300:79–86

    Article  CAS  PubMed  Google Scholar 

  36. Daugaard I, Dominguez D, Kjeldsen TE, Kristensen LS, Hager H, Wojdacz TK et al (2016) Identification and validation of candidate epigenetic biomarkers in lung adenocarcinoma. Sci Rep 6:35807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. de Fraipont F, Moro-Sibilot D, Michelland S, Brambilla E, Brambilla C, Favrot MC (2005) Promoter methylation of genes in bronchial lavages: a marker for early diagnosis of primary and relapsing non-small cell lung cancer? Lung Cancer 50:199–209

    Article  PubMed  Google Scholar 

  38. Dela Cruz CS, Tanoue LT, Matthay RA (2011) Lung cancer: epidemiology, etiology, and prevention. Clin Chest Med 32:605–644

    Article  Google Scholar 

  39. Dent AG, Sutedja TG, Zimmerman PV (2013) Exhaled breath analysis for lung cancer. J Thorac Dis 5(Suppl 5):S540–S550

    PubMed  PubMed Central  Google Scholar 

  40. Destro A, Bianchi P, Alloisio M, Laghi L, Di Gioia S, Malesci A et al (2004) K-ras and p16(INK4A)alterations in sputum of NSCLC patients and in heavy asymptomatic chronic smokers. Lung Cancer 44(1):23–32

    Article  CAS  PubMed  Google Scholar 

  41. Diaz-Lagares J, Mendez-Gonzalez D, Hervas M, Saigi MJ, Pajares D, Garcia AB et al (2016) A novel epigenetic signature for early diagnosis in lung cancer. Clin Cancer Res 22(13):3361–3371

    Article  CAS  PubMed  Google Scholar 

  42. Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M et al (2008) Circulating mutant DNA to assess tumor dynamics. Nat Med 14:985–990

    Article  CAS  PubMed  Google Scholar 

  43. Dietrich D, Kneip C, Raji O, Liloglou T, Seegebarth A, Schlegel T et al (2012) Performance evaluation of the DNA methylation biomarker SHOX2 for the aid in diagnosis of lung cancer based on the analysis of bronchial aspirates. Int J Oncol 40:825–832

    CAS  PubMed  Google Scholar 

  44. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M et al (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38:1378–1385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Ellinger J, Kahl P, von der Gathen J, Rogenhofer S, Heukamp LC, Gutgemann I et al (2010) Global levels of histone modifications predict prostate cancer recurrence. Prostate 70:61–69

    Article  CAS  PubMed  Google Scholar 

  46. Estécio MR, Yan PS, Ibrahim AE, Tellez CS, Shen L, Huang TH et al (2007) High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res 17:1529–1536

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Fabbri M, Garzon R, Cimmino A, Liu Z, Zanesi N, Callegari E et al (2007) MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc Natl Acad Sci U S A 104:15805–15810

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Fang JY, Xiao SD (2003) Folic acid, polymorphism of methyl-group metabolism genes, and DNA methylation in relation to GI carcinogenesis. J Gastroenterol 38:821–829

    Article  CAS  PubMed  Google Scholar 

  49. Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89–92

    Article  CAS  PubMed  Google Scholar 

  50. Feng Q, Hawes SE, Stern JE, Wiens L, Lu H, Dong ZM et al (2008) DNA methylation in tumor and matched normal tissues from non-small cell patients with lung cancer. Cancer Epidemiol Biomarkers Prev 17:645–654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Feng N, Ching T, Wang Y, Liu B, Lin H, Shi O et al (2016) Analysis of microarray data on gene expression and methylation to identify long non-coding RNAs in non-small cell lung cancer. Sci Rep 6:37233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Field JK, Baldwin D, Brain K, Devaraj A, Eisen T, Duffy SW et al (2011) CT screening for lung cancer in the UK: position statement by UKLS investigators following the NLST report. Thorax 66:736–737

    Article  PubMed  Google Scholar 

  53. Fillmore CM, Xu C, Desai PT, Berry JM, Rowbotham SP, Lin Y-J et al (2015) EZH2 inhibition sensitizes BRG1 and EGFR mutant lung tumours to TopoII inhibitors. Nature 520:239–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Fischer JR, Ohnmacht U, Rieger N, Zemaitis M, Stoffregen C, Manegold C et al (2007) Prognostic significance of RASSF1A promoter methylation on survival of non-small cell patients with lung cancer treated with gemcitabine. Lung Cancer 56:115–123

    Article  PubMed  Google Scholar 

  55. Forde PM, Brahmer JR, Kelly RJ (2014) New strategies in lung cancer: epigenetic therapy for non-small cell lung cancer. Clin Cancer Res 20:2244–2248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Fu J, Qin L, He T, Qin J, Hong J, Wong J et al (2011) The TWIST/Mi2/NuRD protein complex and its essential role in cancer metastasis. Cell Res 21(2):275–289

    Article  CAS  PubMed  Google Scholar 

  57. Gaudet F, Hodgson JG, Eden A, Jackson-Grusby L, Dausman J, Gray JW et al (2003) Induction of tumors in mice by genomic hypomethylation. Science 300(5618):489–492

    Article  CAS  PubMed  Google Scholar 

  58. Glazer CA, Smith IM, Ochs MF, Begum S, Westra W, Chang SS et al (2009) Integrative discovery of epigenetically derepressed cancer testis antigens in NSCLC. PLoS One 4:e8189

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  59. Gu J, Berman D, Lu C, Wistuba II, Roth JA, Frazier M et al (2006) Aberrant promoter methylation profile and association with survival in patients with non-small cell lung cancer. Clin Cancer Res 12:7329–7338

    Article  CAS  PubMed  Google Scholar 

  60. Gu Y, Wang C, Wang Y, Qiu X, Wang E (2009) Expression of thymosin beta10 and its role in non-small cell lung cancer. Hum Pathol 40:117–124

    Article  CAS  PubMed  Google Scholar 

  61. Gupta PK, Sahota A, Boyadjiev SA, Bye S, Shao C, O’Neill JP et al (1997) High frequency in vivo loss of heterozygosity is primarily a consequence of mitotic recombination. Cancer Res 57(6):1188–1193

    CAS  PubMed  Google Scholar 

  62. Han W, Wang T, Reilly AA, Keller SM, Spivack SD (2009) Gene promoter methylation assayed in exhaled breath, with differences in smokers and lung cancer patients. Respir Res 10:86

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  63. Han Y, Shi K, Zhou SJ, Yu DP, Liu ZD (2016) The clinicopathological significance of hMLH1 hypermethylation in non-small-cell lung cancer: a meta-analysis and literature review. Onco Targets Ther 9:5081–5090

    Article  PubMed  PubMed Central  Google Scholar 

  64. Han M, Xu W, Cheng P, Jin H, Wang X (2017) Histone demethylase lysine demethylase 5B in development and cancer. Oncotarget 8(5):8980–8991

    PubMed  Google Scholar 

  65. Hayami S, Yoshimatsu M, Veerakumarasivam A, Unoki M, Iwai Y, Tsunoda T et al (2010) Overexpression of the JmjC histone demethylase KDM5B in human carcinogenesis: involvement in the proliferation of cancer cells through the E2F/RB pathway. Mol Cancer 9:59

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  66. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD et al (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39:311–318

    Article  CAS  PubMed  Google Scholar 

  67. Hiddinga BI, Pauwels P, Janssens A, van Meerbeeck JP (2016) O6-Methylguanine-DNA methyltransferase (MGMT): a drugable target in lung cancer? Lung Cancer. pii:S0169-5002(16)30412-3

    Google Scholar 

  68. Hoffman PC, Mauer AM, Vokes EE (2000) Lung cancer. Lancet 355:479–485

    Article  CAS  PubMed  Google Scholar 

  69. Holt D, Dreimanis M, Pfeiffer M, Firgaira F, Morley A, Turner D (1999) Interindividual variation in mitotic recombination. Am J Hum Genet 65(5):1423–1427

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Hong JA, Kang Y, Abdullaev Z et al (2005) Reciprocal binding of CTCF and BORIS to the NY-ESO-1 promoter coincides with derepression of this cancer-testis gene in lung cancer cells. Cancer Res 65:7763–7774

    Article  CAS  PubMed  Google Scholar 

  71. Hong YS, Roh MS, Kim NY et al (2007) Hypermethylation of p16INK4a in Korean non-small cell patients with lung cancer. J Korean Med Sci 22:S32–S37

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Hoque MO, Kim MS, Ostrow KL et al (2008) Genomewide promoter analysis uncovers portions of the cancer methylome. Cancer Res 68:2661–2670

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Houseman EA, Accomando WP, Koestler DC et al (2012) DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 13:86

    Article  PubMed  PubMed Central  Google Scholar 

  74. Hsu HS, Chen TP, Hung CH, Wen CK, Lin RK, Lee HC et al (2007) Characterization of a multiple epigenetic marker panel for lung cancer detection and risk assessment in plasma. Cancer 110(9):2019–2026

    Article  CAS  PubMed  Google Scholar 

  75. Hu YC, Sidransky D, Ahrendt SA (2002) Molecular detection approachesνfor smoking associated tumors. Oncogene 21:ν7289–ν7297

    Article  CAS  Google Scholar 

  76. Hua F, Fang N, Li X, Zhu S, Zhang W, Gu J (2014) A meta analysis of the relationship between RARb Gene promoter methylation and non-small cell lung cancer. PLoS One 9(5):e96163

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  77. Hubers AJ, Brinkman P, Boksem RJ, Rhodius RJ, Witte BI, Zwinderman AH et al (2014) Combined sputum hypermethylation and eNose analysis for lung cancer diagnosis. J Clin Pathol 67(8):707–711

    Article  PubMed  Google Scholar 

  78. Imre G, Gekeler V, Leja A et al (2006) Histone deacetylase inhibitors suppress the inducibility of nuclear factor kappaB by tumor necrosis factor-alpha receptor-1 downregulation. Cancer Res 66:5409–5418

    Article  CAS  PubMed  Google Scholar 

  79. Isbell JM, Deppen S, Putnam JB Jr et al (2011) Existing general population models inaccurately predict lung cancer risk in patients referred for surgical evaluation. Ann Thorac Surg 91:227–233

    Article  PubMed  PubMed Central  Google Scholar 

  80. Ito M, Ito G, Kondo M et al (2005) Frequent inactivation of RASSF1A, BLU, and SEMA3B on 3p21.3 by promoter hypermethylation and allele loss in non-small cell lung cancer. Cancer Lett 225:131–139

    Article  CAS  PubMed  Google Scholar 

  81. Jang SJ, Soria JC, Wang L et al (2001) Activation of melanoma antigen tumor antigens occurs early in lung carcinogenesis. Cancer Res 61:7959–7963

    CAS  PubMed  Google Scholar 

  82. Johnstone RW (2002) Histone-deacetylase inhibitors: novel drugs for the treatment of cancer. Nat Rev Drug Discov 1:287–299

    Article  CAS  PubMed  Google Scholar 

  83. Jones PA, Baylin SB (2002) The fundamental role of epigenetic events in cancer. Nat Rev Genet 3:415–428

    Article  CAS  PubMed  Google Scholar 

  84. Juergens RA, Wrangle J, Vendetti FP et al (2011) Combination epigenetic therapy has efficacy in patients with refractory advanced non-small cell lung cancer. Cancer Discov 1:598–607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Kalluri R, Weinberg RA (2009) The basics of epithelialmesenchymal transition. J Clin Invest 119(6):1420–1428

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Kayser G, Sienel W, Kubitz B et al (2011) Poor outcome in primary non-small cell lung cancers is predicted by transketolase TKTL1 expression. Pathology 43:719–724

    Article  PubMed  Google Scholar 

  87. Ke XS, Qu Y, Rostad K, Li WC, Lin B, Halvorsen OJ et al (2009) Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis. PLoS One 4:e4687

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  88. Kelsey CR, Marks LB, Hollis D et al (2009) Local recurrence after surgery for early stage lung cancer: an 11-year experience with 975 patients. Cancer 115:5218–5227

    Article  PubMed  Google Scholar 

  89. Khaled MA, Krumdieck CL (1985) Association of folate molecules as determined by proton NMR: implications on enzyme binding. Biochem Biophys Res Commun 130:1273–1280

    Article  CAS  PubMed  Google Scholar 

  90. Kim DH, Nelson HH, Wiencke JK et al (2001) p16(INK4a) and histology-specific methylation of CpG islands by exposure to tobacco smoke in non-small cell lung cancer. Cancer Res 61:3419–3424

    CAS  PubMed  Google Scholar 

  91. Kim H, Kwon YM, Kim JS et al (2004) Tumor-specific methylation in bronchial lavage for the early detection of non-small-cell lung cancer. J Clin Oncol 22:2363–2370

    Article  CAS  PubMed  Google Scholar 

  92. Kim JS, Han J, Shim YM, Park J, Kim DH (2005) Aberrant methylation of H-cadherin (CDH13) promoter is associated with tumor progression in primary nonsmall cell lung carcinoma. Cancer 104(9):1825–1833

    Article  CAS  PubMed  Google Scholar 

  93. Kim H, Kwon YM, Kim JS et al (2006a) Elevated mRNA levels of DNA methyltransferase-1 as an independent prognostic factor in primary nonsmall cell lung cancer. Cancer 107:1042–1049

    Article  CAS  PubMed  Google Scholar 

  94. Kim HR, Kim EJ, Yang SH et al (2006b) Trichostatin A induces apoptosis in lung cancer cells via simultaneous activation of the death receptor-mediated and mitochondrial pathway? Exp Mol Med 38:616–624

    Article  CAS  PubMed  Google Scholar 

  95. Kim JS, Kim JW, Han J, Shim YM, Park J, Kim DH (2006c) Cohypermethylation of p16 and FHIT promoters as a prognostic factor of recurrence in surgically resected stage I non-small cell lung cancer. Cancer Res 66:4049–4054

    Article  CAS  PubMed  Google Scholar 

  96. Kim DS, Kim MJ, Lee JY, Kim YZ, Kim EJ, Park JY (2007) Aberrant methylation of E-cadherin and H-cadherin genes in nonsmall cell lung cancer and its relation to clinicopathologic features. Cancer 110:2785–2792

    Article  CAS  PubMed  Google Scholar 

  97. Kim SH, Lee S, Lee CH et al (2009) Expression of cancer-testis antigens MAGE-A3/6 and NY-ESO-1 in non-small-cell lung carcinomas and their relationship with immune cell infiltration. Lung 187:401–411

    Article  CAS  PubMed  Google Scholar 

  98. Kimura H (2013) Histone modifications for human epigenome analysis. J Hum Genet 58:439–445

    Article  CAS  PubMed  Google Scholar 

  99. Kneip C, Schmidt B, Seegebarth A et al (2011) SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer in plasma. J Thorac Oncol 6:1632–1638

    Article  PubMed  Google Scholar 

  100. Komatsu N, Kawamata N, Takeuchi S et al (2006) SAHA, a HDAC inhibitor, has profound anti-growth activity against non-small cell lung cancer cells. Oncol Rep 15:187–191

    CAS  PubMed  Google Scholar 

  101. Kondo M, Suzuki H, Ueda R et al (1995) Frequent loss of imprinting of the H19 gene is often associated with its overexpression in human lung cancers. Oncogene 10:1193–1198

    CAS  PubMed  Google Scholar 

  102. Konecny M, Markus J, Waczulikova I et al (2016) The value of SHOX2 methylation test in peripheral blood samples used for the differential diagnosis of lung cancer and other lung disorders. Neoplasma 63:246–253

    CAS  PubMed  Google Scholar 

  103. Kristensen LH, Nielsen AL, Helgstrand C, Lees M, Cloos P, Kastrup JS et al (2012) Studies of H3K4me3 demethylation by KDM5B/Jarid1B/PLU1 reveals strong substrate recognition in vitro and identifies 2,4-pyridine-dicarboxylic acid as an in vitro and in cell inhibitor. FEBS J 279:1905–1914

    Article  CAS  PubMed  Google Scholar 

  104. Kun N, Yujie J, Xuezhu Z (2015) Cell-free circulating tumor DNA in plasma/serum of non-small cell lung cancer. Tumour Biol 36(1):7–19

    Article  CAS  Google Scholar 

  105. Labbé RM, Holowatyj A, Yang ZQ (2013) Histone lysine demethylase (KDM) subfamily 4: structures, functions and therapeutic potential. Am J Transl Res 6:1–15

    PubMed  PubMed Central  Google Scholar 

  106. Lander ES, Linton LM, Birren B et al (2009) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921

    Article  Google Scholar 

  107. Langevin SM, Kelsey KT (2013) The fate is not always written in the genes: epigenomics in epidemiologic studies. Environ Mol Mutagen 54:533–541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Langevin SM, Kratzke RA, Kelsey KT (2015) Epigenetics of lung cancer. Transl Res 165(1):74–90

    Article  CAS  PubMed  Google Scholar 

  109. Le Bras GF, Taubenslag KJ, Andl CD (2012) The regulation of cell-cell adhesion during epithelial-mesenchymal transition, motility and tumor progression. Cell Adh Migr 6(4):365–373

    Article  PubMed  PubMed Central  Google Scholar 

  110. Lee SM, Park JY, Kim DS (2012 Aug) Methylation of TMEFF2 gene in tissue and serum DNA from patients with non-small cell lung cancer. Mol Cells 34(2):171–176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Leng S, Do K, Yingling CM et al (2012) Defining a gene promoter methylation signature in sputum for lung cancer risk assessment. Clin Cancer Res 18:3387–3395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Lenka G, Tsai MH, Lin HC, Hsiao JH, Lee YC, Lu TP et al (2017) Identification of methylation- driven, differentially expressed STXBP6 as a novel biomarker in lung adenocarcinoma. Sci Rep 7:42573

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Li CT, Hsiao YM, Wu TC et al (2011) Vorinostat, SAHA, represses telomerase activity via epigenetic regulation of telomerase reverse transcriptase in non-small cell lung cancer cells. J Cell Biochem 112:3044–3053

    Article  CAS  PubMed  Google Scholar 

  114. Li X, Su Y, Pan J, Zhou Z, Song B, Xiong E et al (2013) Connexin 26 is down-regulated by KDM5B in the progression of bladder cancer. Int J Mol Sci 14:7866–7879

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  115. Licchesi JD, Westra WH, Hooker CM, Herman JG (2008) Promoter hypermethylation of hallmark cancer genes in atypical adenomatous hyperplasia of the lung. Clin Cancer Res 14:2570–2578

    Article  CAS  PubMed  Google Scholar 

  116. Lin RK, Hsu HS, Chang JW, Chen CY, Chen JT, Wang YC (2007) Alteration of DNA methyltransferases contributes to 5’CpG methylation and poor prognosis in lung cancer. Lung Cancer 55:205–213

    Article  PubMed  Google Scholar 

  117. Lin Q, Geng J, Ma K, Yu J, Sun J, Shen Z et al (2009) RASSF1A, APC, ESR1, ABCB1 and HOXC9, but not p16INK4A, DAPK1, PTEN and MT1G genes were frequently methylated in the stage I non-small cell lung cancer in China. J Cancer Res Clin Oncol 135(12):1675–1684

    Article  CAS  PubMed  Google Scholar 

  118. Lin RK, Hsieh YS, Lin P et al (2010a) The tobacco-specific carcinogen NNK induces DNA methyltransferase 1 accumulation and tumor suppressor gene hypermethylation in mice and lung cancer patients. J Clin Invest 120:521–532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Lin RK, Wu CY, Chang JW et al (2010b) Dysregulation of p53/Sp1 control leads to DNA methyltransferase-1 overexpression in lung cancer. Cancer Res 70:5807–5817

    Article  CAS  PubMed  Google Scholar 

  120. Lin SH, Wang J, Saintigny P, Wu CC, Giri U, Zhang J et al (2014) Genes suppressed by DNA methylation in non-small cell lung cancer reveal the epigenetics of epithelialmesenchymal transition. BMC Genomics 15:1079

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  121. Lissa D, Robles AI (2016) Methylation analyses in liquid biopsy. Transl Lung Cancer Res 5(5):492–504

    Article  PubMed  PubMed Central  Google Scholar 

  122. Liu Y, An Q, Li L, Zhang D, Huang J, Feng X et al (2003) Hypermethylation of p16INK4a in Chinese lung cancer patients: biological and clinical implications. Carcinogenesis 24(12):1897–1901

    Article  CAS  PubMed  Google Scholar 

  123. Liu Y, Lan Q, Siegfried JM, Luketich JD, Keohavong P (2006) Aberrant promoter methylation of p16 and MGMT genes in lung tumors from smoking and never-smoking patients with lung cancer. Neoplasia 8:46–51

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Liu Z, Zhao J, Chen XF et al (2008) CpG island methylator phenotype involving tumor suppressor genes located on chromosome 3p in non-small cell lung cancer. Lung Cancer 62:15–22

    Article  CAS  PubMed  Google Scholar 

  125. Liu F, Killian JK, Yang M et al (2010a) Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate. Oncogene 29:3650–3664

    Article  CAS  PubMed  Google Scholar 

  126. Liu Z, Li W, Lei Z et al (2010b) CpG island methylator phenotype involving chromosome 3p confers an increased risk of nonsmall cell lung cancer. J Thorac Oncol 5:790–797

    Article  PubMed  Google Scholar 

  127. Liu WB, Han F, Jiang X, Chen HQ, Zhao H, Liu Y et al (2015) TMEM196 acts as a novel functional tumour suppressor inactivated by DNA methylation and is a potential prognostic biomarker in lung cancer. Oncotarget 6(25):21225–21239

    Article  PubMed  PubMed Central  Google Scholar 

  128. Lujambio A, Portela A, Liz J, Melo SA, Rossi S, Spizzo R et al (2010) CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer. Oncogene 29(48):6390–6401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Machida EO, Brock MV, Hooker CM et al (2006) Hypermethylation of ASC/TMS1 is a sputum marker for late-stage lung cancer. Cancer Res 66:6210–6218

    Article  CAS  PubMed  Google Scholar 

  130. Margaritis T, Oreal V, Brabers N, Maestroni L, Vitaliano-Prunier A, Benschop JJ et al (2012) Two distinct repressive mechanisms for histone 3 lysine 4 methylation through promoting 3′-end antisense transcription. PLoS Genet 8:e1002952

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Marsit CJ, Houseman EA, Christensen BC et al (2006) Examination of a CpG island methylator phenotype and implications of methylation profiles in solid tumors. Cancer Res 66:10621–10629

    Article  CAS  PubMed  Google Scholar 

  132. Martin C, Zhang Y (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6:838–849

    Article  CAS  PubMed  Google Scholar 

  133. Marwick JA, Kirkham PA, Stevenson CS et al (2004) Cigarette smoke alters chromatin remodeling and induces proinflammatory genes in rat lungs. Am J Respir Cell Mol Biol 31:633–642

    Article  CAS  PubMed  Google Scholar 

  134. Massion PP, Carbone DP (2003) The molecular basis of lung cancer: molecular abnormalities and therapeutic implications. Respir Res 4:12

    Article  PubMed  PubMed Central  Google Scholar 

  135. Mehta A, Dobersch S, Romero-Olmedo AJ, Barreto G (2015) Epigenetics in lung cancer diagnosis and therapy. Cancer Metastasis Rev 34:229–241

    Article  CAS  PubMed  Google Scholar 

  136. Meng X, Riordan NH (2006) Cancer is a functional repair tissue. Med Hypotheses 66:486–490

    Article  CAS  PubMed  Google Scholar 

  137. Minamiya Y, Ono T, Saito H et al (2010) Strong expression of HDAC3 correlates with a poor prognosis in patients with adenocarcinoma of the lung. Tumour Biol 31:533–539

    Article  CAS  PubMed  Google Scholar 

  138. Minamiya Y, Ono T, Saito H et al (2011) Expression of histone deacetylase 1 correlates with a poor prognosis in patients with adenocarcinoma of the lung. Lung Cancer 74:300–304

    Article  PubMed  Google Scholar 

  139. Miyanaga A, Gemma A, Noro R et al (2008) Antitumor activity of histone deacetylase inhibitors in non-small cell lung cancer cells: development of a molecular predictive model. Mol Cancer Ther 7:1923–1930

    Article  CAS  PubMed  Google Scholar 

  140. Mungall AJ, Palmer SA, Sims SK et al (2003) The DNA sequence and analysis of human chromosome 6. Nature 425:805–811

    Article  CAS  PubMed  Google Scholar 

  141. Nadal-Ribelles M, Mas G, Millan-Zambrano G, Sole C, Ammerer G, Chavez S et al (2015) H3K4 monomethylation dictates nucleosome dynamics and chromatin remodeling at stress-responsive genes. Nucleic Acids Res 43:4937–4949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Niklinska W, Naumnik W, Sulewska A, Kozłowski M, Pankiewicz W, Milewski R (2009) Prognostic significance of DAPK and RASSF1A promoter hypermethylation in non-small cell lung cancer (NSCLC). Folia Histochem Cytobiol 47(2):275–280

    Article  CAS  PubMed  Google Scholar 

  143. Northrop-Clewes CA, Thurnham DI (2007) Monitoring micronutrients in cigarette smokers. Clin Chim Acta 377:14–38

    Article  CAS  PubMed  Google Scholar 

  144. O’Hagan HM, Wang W, Sen S et al (2011) Oxidative damage targets complexes containing DNA methyltransferases, SIRT1, and polycomb members to promoter CpG Islands. Cancer Cell 20:606–619

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  145. Ortega RM, Lopez-Sobaler AM, Gonzalez-Gross MM et al (1994) Influence of smoking on folate intake and blood folate concentrations in a group of elderly Spanish men. J Am Coll Nutr 13:68–72

    Article  CAS  PubMed  Google Scholar 

  146. Ota N, Kawakami K, Okuda T et al (2006) Prognostic significance of p16(INK4a) hypermethylation in non-small cell lung cancer is evident by quantitative DNA methylation analysis. Anticancer Res 26:3729–3732

    CAS  PubMed  Google Scholar 

  147. OzdaÄŸ H, Teschendorff AE, Ahmed AA et al (2006) Differential expression of selected histone modifier genes in human solid cancers. BMC Genomics 7:90

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  148. Palmisano WA, Divine KK, Saccomanno G et al (2000) Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Res 60:5954–5958

    CAS  PubMed  Google Scholar 

  149. Palmisano WA, Crume KP, Grimes MJ et al (2003) Aberrant promoter methylation of the transcription factor genes PAX5 alpha and beta in human cancers. Cancer Res 63:4620–4625

    CAS  PubMed  Google Scholar 

  150. Patel K, Dickson J, Din S et al (2010) Targeting of 5-aza-2′- deoxycytidine residues by chromatin-associated DNMT1 induces proteasomal degradation of the free enzyme. Nucleic Acids Res 38:4313–4324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Pinskaya M, Morillon A (2009) Histone H3 lysine 4 di-methylation: a novel mark for transcriptional fidelity? Epigenetics 4:302–306

    Article  CAS  PubMed  Google Scholar 

  152. Piyathilake CJ, Macaluso M, Hine RJ, Richards EW, Krumdieck CL (1994) Local and systemic effects of cigarette smoking on folate and vitamin B-12. Am J Clin Nutr 60:559–566

    CAS  PubMed  Google Scholar 

  153. Poirier JT, Gardner EE, Connis N, Moreira AL, de Stanchina E, Hann CL et al (2015) DNA methylation in small cell lung cancer defines distinct disease subtypes and correlates with high expression of EZH2. Oncogene 34(48):5869–5878

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Ponomaryova AA, Rykova EY, Cherdyntseva NV et al (2013) Potentialities of aberrantly methylated circulating DNA for diagnostics and post-treatment follow-up of lung cancer patients. Lung Cancer 81:397–403

    Article  PubMed  Google Scholar 

  155. Powrózek T, Krawczyk P, Kucharczyk T et al (2014) Septin 9 promoter region methylation in free circulating DNA-potential role in noninvasive diagnosis of lung cancer: preliminary report. Med Oncol 31:917

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  156. Powrozek T, Krawczyk P, Nicos M, Kuznar-Kaminska B, Batura-Gabryel H, Milanowski J (2016) Methylation of the DCLK1 promoter region in circulating free DNA and its prognostic value in lung cancer patients. Clin Transl Oncol 18:398–404

    Article  CAS  PubMed  Google Scholar 

  157. Pu W, Geng X, Chen S, Tan L, Tan Y, Wang A et al (2016) Aberrant methylation of CDH13 can be a diagnostic biomarker for lung adenocarcinoma. J Cancer 7(15):2280–2289

    Article  PubMed  PubMed Central  Google Scholar 

  158. Pulling LC, Divine KK, Klinge DM, Gilliland FD, Kang T, Schwartz AG et al (2003) Promoter hypermethylation of the O6- methylguanine-DNA methyltransferase gene: more common in lung adenocarcinomas from never-smokers than smokers and associated with tumor progression. Cancer Res 63(16):4842–4848

    CAS  PubMed  Google Scholar 

  159. Qin H, Zhu J, Zeng Y et al (2017) Aberrant promoter methylation of hOGG1 may be associated with increased risk of non-small cell lung cancer. Oncotarget 8(5):8330–8341

    PubMed  Google Scholar 

  160. Radhakrishnan VM, Jensen TJ, Cui H, Futscher BW, Martinez JD (2011) Hypomethylation of the 14-3-3sigma promoter leads to increased expression in non-small cell lung cancer. Genes Chromosom Cancer 50:830–836

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Raji OY, Duffy SW, Agbaje OF et al (2012) Predictive accuracy of the Liverpool lung project risk model for stratifying patients for computed tomography screening for lung cancer: a case–control and cohort validation study. Ann Intern Med 157(4):242–250

    Article  PubMed  PubMed Central  Google Scholar 

  162. Ramakrishnan S, Pokhrel S, Palani S, Pflueger C, Parnell TJ, Cairns BR et al (2016) Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription. Nat Commun 7:11949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Ramirez JL, Rosell R, Taron M et al (2005) 14-3-3sigma methylation in pretreatment serum circulating DNA of cisplatin-plus-gemcitabine-treated advanced non-small-cell lung cancer patients predicts survival: the Spanish Lung Cancer Group. J Clin Oncol 23:9105–9112

    Article  CAS  PubMed  Google Scholar 

  164. Rattray NJ, Hamrang Z, Trivedi DK, Goodacre R, Fowler SJ (2014) Taking your breath away: metabolomics breathes life in to personalized medicine. Trends Biotechnol 32(10):538–548

    Article  CAS  PubMed  Google Scholar 

  165. Rauch T, Wang Z, Zhang X et al (2007) Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci U S A 104:5527–5532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Rauch TA, Zhong X, Wu X et al (2008) High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc Natl Acad Sci U S A 105:252–257

    Article  CAS  PubMed  Google Scholar 

  167. Renaud S, Pugacheva EM, Delgado MD et al (2007) Expression of the CTCF-paralogous cancer-testis gene, brother of the regulator of imprinted sites (BORIS), is regulated by three alternative promoters modulated by CpG methylation and by CTCF and p53 transcription factors. Nucl Acids Res 35:7372–7388

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Richardson F, Young GD, Sennello R, Wolf J, Argast GM, Mercado P et al (2012) The evaluation of E-Cadherin and vimentin as biomarkers of clinical outcomes among patients with non-small cell lung cancer treated with erlotinib as second- or third-line therapy. Anticancer Res 32(2):537–552

    CAS  PubMed  Google Scholar 

  169. Russo AL, Thiagalingam A, Pan H, Califano J, Cheng KH, Ponte JF et al (2005) Differential DNA hypermethylation of critical genes mediates the stage-specific tobacco smoke-induced neoplastic progression of lung cancer. Clin Cancer Res 11(7):2466–2470

    Article  CAS  PubMed  Google Scholar 

  170. Salazar F, Molina MA, Sanchez-Ronco M et al (2011) First-line therapy and methylation status of CHFR in serum influence outcome to chemotherapy versus EGFR tyrosine kinase inhibitors as second-line therapy in stage IV non-small-cell lung cancer patients. Lung Cancer 72:84–91

    Article  PubMed  Google Scholar 

  171. Sasaki H, Moriyama S, Nakashima Y et al (2004) Histone deacetylase 1 mRNA expression in lung cancer. Lung Cancer 46:171–178

    Article  PubMed  Google Scholar 

  172. Schiffmann I, Greve G, Jung M, Lübbert M (2016) Epigenetic therapy approaches in non-small cell lung cancer: update and perspectives. Epigenetics 11(12):858–870

    Article  PubMed  Google Scholar 

  173. Schlensog M, Magnus L, Heide T, Eschenbruch J, Steib F, Tator M et al (2016) Epigenetic loss of putative tumor suppressor SFRP3 correlates with poor prognosis of lung adenocarcinoma patients. Epigenetics

    Google Scholar 

  174. Schmidt B, Beyer J, Dietrich D et al (2015) Quantification of cell-free mSHOX2 plasma DNA for therapy monitoring in advanced stage non-small cell (NSCLC) and small-cell lung cancer (SCLC) patients. PLoS One 10:e0118195

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  175. Schmiemann V, Bocking A, Kazimirek M et al (2005) Methylation assay for the diagnosis of lung cancer on bronchial aspirates: a cohort study. Clin Cancer Res 11:7728–7734

    Article  CAS  PubMed  Google Scholar 

  176. Schuebel KE, Chen W, Cope L et al (2007) Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet 3:1709–1723

    Article  CAS  PubMed  Google Scholar 

  177. Selamat SA, Galler JS, Joshi AD et al (2011) DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma. PLoS One 6:e21443

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Seligson DB, Horvath S, McBrian MA et al (2009) Global levels of histone modifications predict prognosis in different cancers. Am J Pathol 174:1619–1628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. Seng TJ, Currey N, Cooper WA et al (2008) DLEC1 and MLH1 promoter methylation are associated with poor prognosis in non-small cell lung carcinoma. Br J Cancer 99:375–382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Seo SK, Jin HO, Woo SH et al (2011) Histone deacetylase inhibitors sensitize human non-small cell lung cancer cells to ionizing radiation through acetyl p53-mediated c-myc down-regulation. J Thorac Oncol 6:1313–1319

    Article  PubMed  Google Scholar 

  181. Shackelford RE, Kaufmann WK, Paules RS (1999) Cell cycle control, checkpoint mechanisms, and genotoxic stress. Environ Health Perspect 107(Suppl 1):5–24

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Shames DS, Girard L, Gao B et al (2006) A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med 3:e486

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  183. Shen X, Zhuang Z, Zhang Y, Chen Z, Shen L, Pu W et al (2015) JARID1B modulates lung cancer cell proliferation and invasion by regulating p53 expression. Tumour Biol 36:7133–7142

    Article  CAS  PubMed  Google Scholar 

  184. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA et al (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941–953

    Article  CAS  PubMed  Google Scholar 

  185. Shiba-Ishii A, Noguchi M (2012) Aberrant stratifin overexpression is regulated by tumor-associated CpG demethylation in lung adenocarcinoma. Am J Pathol 180:1653–1662

    Article  CAS  PubMed  Google Scholar 

  186. Shinjo K, Okamoto Y, An B et al (2012) Integrated analysis of genetic and epigenetic alterations reveals CpG island methylator phenotype associated with distinct clinical characters of lung adenocarcinoma. Carcinogenesis 33:1277–1285

    Article  CAS  PubMed  Google Scholar 

  187. Shoji F, Haro A, Yoshida T et al (2010) Prognostic significance of intratumoral blood vessel invasion in pathologic stage IA non-small cell lung cancer. Ann Thorac Surg 89:864–869

    Article  PubMed  Google Scholar 

  188. Siegel R, Naishadham D, Jemal A (2013) Cancer statistics, 2013. CA Cancer J Clin 63:11–30

    Article  PubMed  Google Scholar 

  189. Simkin M, Abdalla M, El-Mogy M, Haj-Ahmad Y (2012) Differences in the quantity of DNA found in the urine and saliva of smokers versus nonsmokers: implications for the timing of epigenetic events. Epigenomics 4:343–352

    Article  CAS  PubMed  Google Scholar 

  190. Singh A, Settleman J (2010) EMT, cancer stem cells and drug resistance: an emerging axis of evil in the war on cancer. Oncogene 29(34):4741–4751

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Smith LT, Lin M, Brena RM et al (2006) Epigenetic regulation of the tumor suppressor gene TCF21 on 6q23-q24 in lung and head and neck cancer. Proc Natl Acad Sci U S A 103:982–987

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Soini Y, Kosma VM, Pirinen R (2015) KDM4A, KDM4B and KDM4C in non-small cell lung cancer. Int J Clin Exp Pathol 8(10):12922–12928

    PubMed  PubMed Central  Google Scholar 

  193. Strauss GM, Herndon JE 2nd, Maddaus MA et al (2008) Adjuvant paclitaxel plus carboplatin compared with observation in stage IB non-small-cell lung cancer: CALGB 9633 with the Cancer and Leukemia Group B, Radiation Therapy Oncology Group, and North Central Cancer Treatment Group Study Groups. J Clin Oncol 26:5043–5051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. Su Y, Fang HB, Jiang F (2016) Integrating DNA methylation and microRNA biomarkers in sputum for lung cancer detection. Clin Epigenetics 8:109

    Article  PubMed  PubMed Central  Google Scholar 

  195. Suga Y, Miyajima K, Oikawa T, Maeda J, Usuda J, Kajiwara N et al (2008) Quantitative p16 and ESR1 methylation in the peripheral blood of patients with non-small cell lung cancer. Oncol Rep 20(5):1137–1142

    CAS  PubMed  Google Scholar 

  196. Suzuki M, Hao C, Takahashi T et al (2005) Aberrant methylation of SPARC in human lung cancers. Br J Cancer 92:942–948

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Suzuki M, Mohamed S, Nakajima T et al (2008) Aberrant methylation of CXCL12 in non-small cell lung cancer is associated with an unfavorable prognosis. Int J Oncol 33:113–119

    CAS  PubMed  Google Scholar 

  198. Tang X, Khuri FR, Lee JJ et al (2000) Hypermethylation of the deathassociated protein (DAP) kinase promoter and aggressiveness in stage I non-small-cell lung cancer. J Natl Cancer Inst 92:1511–1516

    Article  CAS  PubMed  Google Scholar 

  199. Tekpli X, Skaug V, Bæra R, Phillips DH, Haugen A, Mollerup S (2016) Estrogen receptor expression and gene promoter methylation in non-small cell lung cancer – a short report. Cell Oncol (Dordr) 39(6):583–589

    Article  CAS  Google Scholar 

  200. Thiery JP, Acloque H, Huang RY et al (2009) Epithelial-mesenchymal transitions in development and disease. Cell 139(5):871–890

    Article  CAS  PubMed  Google Scholar 

  201. Thinnes CC, England KS, Kawamura A, Chowdhury R, Schofield CJ, Hopkinson RJ (2014) Targeting histone lysine demethylases-progress, challenges, and the future. Biochim Biophys Acta 1839:1416–1432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Toyooka S, Maruyama R, Toyooka KO et al (2003) Smoke exposure, histologic type and geography-related differences in the methylation profiles of non-small cell lung cancer. Int J Cancer 103:153–160

    Article  CAS  PubMed  Google Scholar 

  203. Toyooka S, Suzuki M, Tsuda T et al (2004) Dose effect of smoking on aberrant methylation in non-small cell lung cancers. Int J Cancer 110:462–464

    Article  CAS  PubMed  Google Scholar 

  204. Toyooka S, Mitsudomi T, Soh J et al (2011) Molecular oncology of lung cancer. Gen Thorac Cardiovasc Surg 59:527–537

    Article  PubMed  Google Scholar 

  205. Toyota M, Ahuja N, Ohe-Toyota M et al (1999) CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci U S A 96:8681–8686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Tsou JA, Galler JS, Siegmund KD, Laird PW, Turla S, Cozen W et al (2007) Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma. Mol Cancer 6:70

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  207. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P et al (2006) Histone demethylation by a family of JmjC domain-containing proteins. Nature 439:811–816

    Article  CAS  PubMed  Google Scholar 

  208. Usadel H, Brabender J, Danenberg KD et al (2002) Quantitative adenomatous polyposis coli promoter methylation analysis in tumor tissue, serum, and plasma DNA of patients with lung cancer. Cancer Res 62:371–375

    CAS  PubMed  Google Scholar 

  209. Vaissiere T, Hung RJ, Zaridze D et al (2009) Quantitative analysis of DNA methylation profiles in lung cancer identifies aberrant DNA methylation of specific genes and its association with gender and cancer risk factors. Cancer Res 69:243–252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  210. Van Den Broeck A, Brambilla E, Moro-Sibilot D et al (2008) Loss of histone H4K20 trimethylation occurs in preneoplasia and influences prognosis of non-small cell lung cancer. Clin Cancer Res 14:7237–7245

    Article  CAS  Google Scholar 

  211. Vasilatos SN, Katz T, Oesterreich S, Wan Y, Davidson NE, Huang Y (2013) Crosstalk between lysine-specific demethylase 1 (LSD1) and histone deacetylases mediates antineoplastic efficacy of HDAC inhibitors in human breast cancer cells. Carcinogenesis 34:1196–1207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Villalba M, Diaz-Lagares A, Redrado M, de Aberasturi AL, Segura V, Bodegas ME et al (2016) Epigenetic alterations leading to TMPRSS4 promoter hypomethylation and protein overexpression predict poor prognosis in squamous lung cancer patients. Oncotarget 7(16):22752–22769

    Article  PubMed  PubMed Central  Google Scholar 

  213. Wang YC, Lu YP, Tseng RC, Lin RK, Chang JW, Chen JT et al (2003) Inactivation of hMLH1 and hMSH2 by promoter methylation in primary non-small cell lung tumors and matched sputum samples. J Clin Invest 111(6):887–895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Wang J, Lee JJ, Wang L et al (2004) Value of p16INK4a and RASSF1A promoter hypermethylation in prognosis of patients with resectable non-small cell lung cancer. Clin Cancer Res 10:6119–6125

    Article  CAS  PubMed  Google Scholar 

  215. Wang M, Vikis HG, Wang Y et al (2007) Identification of a novel tumor suppressor gene p34 on human chromosome 6q25.1. Cancer Res 67:93–99

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Wang H, Zhang B, Chen D et al (2015) Real-time monitoring efficiency and toxicity of chemotherapy in patients with advanced lung cancer. Clin Epigenetics 7:119

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  217. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL et al (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37(8):853–862

    Article  CAS  PubMed  Google Scholar 

  218. Weinberg RA (1995) The retinoblastoma protein and cell cycle control. Cell 81:323–330

    Article  CAS  PubMed  Google Scholar 

  219. Weiner A, Hsieh TH, Appleboim A, Chen HV, Rahat A, Amit I et al (2015) High-resolution chromatin dynamics during a yeast stress response. Mol Cell 58:371–386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  220. Xiang Y, Zhu Z, Han G, Ye X, Xu B, Peng Z et al (2007) JARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancer. Proc Natl Acad Sci U S A 104:19226–19231

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Xiao D, He J (2010) Epithelial mesenchymal transition and lung cancer. J Thorac Dis 2(3):154–159

    CAS  PubMed  PubMed Central  Google Scholar 

  222. Xiao P, Chen JR, Zhou F, Lu CX, Yang Q, Tao GH et al (2014) Methylation of P16 in exhaled breath condensate for diagnosis of non-small cell lung cancer. Lung Cancer 83(1):56–60

    Article  PubMed  Google Scholar 

  223. Xing J, Stewart DJ, Gu J, Lu C, Spitz MR, Wu X (2008) Expression of methylation-related genes is associated with overall survival in patients with non-small cell lung cancer. Br J Cancer 98:1716–1722

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Yamane K, Tateishi K, Klose RJ, Fang J, Fabrizio LA, Erdjument-Bromage H et al (2007) PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol Cell 25:801–812

    Article  CAS  PubMed  Google Scholar 

  225. Yan W, Xu N, Han X, Zhou XM, He B (2016) The clinicopathological significance of FHIT hypermethylation in non-small cell lung cancer, a meta-analysis and literature review. Sci Rep 6:19303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  226. Yanagawa N, Tamura G, Oizumi H et al (2003) Promoter hypermethylation of tumor suppressor and tumor-related genes in non-small cell lung cancers. Cancer Sci 94(7):589–592

    Article  CAS  PubMed  Google Scholar 

  227. Yanagawa N, Tamura G, Oizumi H et al (2007) Promoter hypermethylation of RASSF1A and RUNX3 genes as an independent prognostic prediction marker in surgically resected non-small cell lung cancers. Lung Cancer 58:131–138

    Article  PubMed  Google Scholar 

  228. Yanagawa N, Tamura G, Oizumi H, Endoh M, Sadahiro M, Motoyama T (2011) Inverse correlation between EGFR mutation and FHIT, RASSF1A and RUNX3 methylation in lung adenocarcinoma: relation with smoking status. Anticancer Res 31:1211–1214

    CAS  PubMed  Google Scholar 

  229. Yano M, Toyooka S, Tsukuda K et al (2005) Aberrant promoter methylation of human DAB2 interactive protein (hDAB2IP) gene in lung cancers. Int J Cancer 113:59–66

    Article  CAS  PubMed  Google Scholar 

  230. Yoshino M, Suzuki M, Tian L et al (2009) Promoter hypermethylation of the p16 andWif-1 genes as an independent prognostic marker in stage IA non-small cell lung cancers. Int J Oncol 35:1201–1209

    Article  CAS  PubMed  Google Scholar 

  231. Zhang F, Zhang T, Teng ZH et al (2009) Sensitization to gamma-irradiation-induced cell cycle arrest and apoptosis by the histone deacetylase inhibitor trichostatin A in nonsmall cell lung cancer (NSCLC) cells. Cancer Biol Ther 8:823–831

    Article  CAS  PubMed  Google Scholar 

  232. Zhang Y, Wang R, Song H, Huang G, Yi J, Zheng Y et al (2011) Methylation of multiple genes as a candidate biomarker in non-small cell lung cancer. Cancer Lett 303(1):21–28

    Article  CAS  PubMed  Google Scholar 

  233. Zhang X, Yang X, Wang J, Liang T, Gu Y, Yang D (2015) Down-regulation of PAX6 by promoter methylation is associated with poor prognosis in non small cell lung cancer. Int J Clin Exp Pathol 8(9):11452–11457

    CAS  PubMed  PubMed Central  Google Scholar 

  234. Zhang J, Fu J, Pan Y, Zhang X, Shen L (2016) Silencing of miR-1247 by DNA methylation promoted non-small-cell lung cancer cell invasion and migration by effects of STMN1. Onco Targets Ther 9:7297–7307

    Article  PubMed  PubMed Central  Google Scholar 

  235. Zhou Q, Agoston AT, Atadja P et al (2008) Inhibition of histone deacetylases promotes ubiquitin-dependent proteasomal degradation of DNA methyltransferase 1 in human breast cancer cells. Mol Cancer Res 6:873–883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  236. Zochbauer-Muller S, Minna JD, Gazdar AF (2002) Aberrant DNA methylation in lung cancer: biological and clinical implications. Oncologist 7:451–457

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This manuscript was supported by the IMI contract no. 115749 CANCER-ID (E.L, S.M).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Evi Lianidou .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Mastoraki, S., Lianidou, E. (2017). DNA and Histone Methylation in Lung Cancer. In: Kaneda, A., Tsukada, Yi. (eds) DNA and Histone Methylation as Cancer Targets. Cancer Drug Discovery and Development. Humana Press, Cham. https://doi.org/10.1007/978-3-319-59786-7_15

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-59786-7_15

  • Published:

  • Publisher Name: Humana Press, Cham

  • Print ISBN: 978-3-319-59784-3

  • Online ISBN: 978-3-319-59786-7

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics