418
Views
0
CrossRef citations to date
0
Altmetric
Perspective

Discovery and Development of DNA Methylation-Based Biomarkers for Lung Cancer

, , , , , , , , & show all
Pages 59-72 | Published online: 28 Feb 2014

References

  • Baylin SB . The cancer epigenome: its origins, contributions to tumorigenesis, and translational implications . Proc. Am. Thorac. Soc.9 ( 2 ), 64 – 65 ( 2012 ).
  • Weichenhan D , PlassC . The evolving epigenome . Hum. Mol. Genet.22 ( R1 ), R1 – R6 ( 2013 ).
  • Baer C , ClausR , PlassC . Genome-wide epigenetic regulation of miRNAs in cancer . Cancer Res.73 ( 2 ), 473 – 477 ( 2013 ).
  • Melo SA , EstellerM . Dysregulation of microRNAs in cancer: playing with fire . FEBS Lett.585 ( 13 ), 2087 – 2099 ( 2011 ).
  • Gantier MP , MccoyCE , RusinovaIet al. Analysis of microRNA turnover in mammalian cells following Dicer1 ablation . Nucleic Acids Res.39 ( 13 ), 5692 – 5703 ( 2011 ).
  • Pritchard CC , ChengHH , TewariM . MicroRNA profiling: approaches and considerations . Nat. Rev. Genet.13 ( 5 ), 358 – 369 ( 2012 ).
  • Chen X , BaY , MaLet al. Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases . Cell Res.18 ( 10 ), 997 – 1006 ( 2008 ).
  • Cai J , WuJ , ZhangHet al. miR-186 downregulation correlates with poor survival in lung adenocarcinoma, where it interferes with cell-cycle regulation . Cancer Res.73 ( 2 ), 756 – 766 ( 2013 ).
  • Cao J , SongY , BiNet al. DNA methylation-mediated repression of miR-886-3p predicts poor outcome of human small cell lung cancer . Cancer Res.73 ( 11 ), 3326 – 3335 ( 2013 ).
  • Liloglou T , BediagaNG , BrownBR , FieldJK , DaviesMP . Epigenetic biomarkers in lung cancer . Cancer Lett.342 ( 2 ), 200 – 212 ( 2012 ).
  • Zhu X , LiY , ShenHet al. miR-137 inhibits the proliferation of lung cancer cells by targeting Cdc42 and Cdk6 . FEBS Lett.587 ( 1 ), 73 – 81 ( 2013 ).
  • Wang Z , ChenZ , GaoYet al. DNA hypermethylation of microRNA-34b/c has prognostic value for stage non-small cell lung cancer . Cancer Biol. Ther.11 ( 5 ), 490 – 496 ( 2011 ).
  • Tanaka N , ToyookaS , SohJet al. Frequent methylation and oncogenic role of microRNA-34b/c in small-cell lung cancer . Lung Cancer76 ( 1 ), 32 – 38 ( 2012 ).
  • Heller G , WeinzierlM , NollCet al. Genome-wide miRNA expression profiling identifies miR-9-3 and miR-193a as targets for DNA methylation in non-small cell lung cancers . Clin. Cancer Res.18 ( 6 ), 1619 – 1629 ( 2012 ).
  • Ceppi P , MudduluruG , KumarswamyRet al. Loss of miR-200c expression induces an aggressive, invasive, and chemoresistant phenotype in non-small cell lung cancer . Mol. Cancer Res.8 ( 9 ), 1207 – 1216 ( 2010 ).
  • Tellez CS , JuriDE , DoKet al. EMT and stem cell-like properties associated with miR-205 and miR-200 epigenetic silencing are early manifestations during carcinogen-induced transformation of human lung epithelial cells . Cancer Res.71 ( 8 ), 3087 – 3097 ( 2011 ).
  • Walter K , HolcombT , JanuarioTet al. DNA methylation profiling defines clinically relevant biological subsets of non-small cell lung cancer . Clin. Cancer Res.18 ( 8 ), 2360 – 2373 ( 2012 ).
  • Roybal JD , ZangY , AhnYHet al. miR-200 Inhibits lung adenocarcinoma cell invasion and metastasis by targeting Flt1/VEGFR1 . Mol. Cancer Res.9 ( 1 ), 25 – 35 ( 2011 ).
  • Allis CD , JenuweinT , ReinbergD . Epigenetics . Cold Spring Harbor Laboratory Press , NY, USA ( 2007 ).
  • Easwaran H , JohnstoneSE , Van NesteLet al. A DNA hypermethylation module for the stem/progenitor cell signature of cancer . Genome Res.22 ( 5 ), 837 – 849 ( 2012 ).
  • You JS , JonesPA . Cancer genetics and epigenetics: two sides of the same coin?Cancer Cell22 ( 1 ), 9 – 20 ( 2012 ).
  • Liu J , LeeW , JiangZet al. Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events . Genome Res.22 ( 12 ), 2315 – 2327 ( 2012 ).
  • Rodriguez-Paredes M , MartinezDe Paz A , Simo-RiudalbasLet al. Gene amplification of the histone methyltransferase SETDB1 contributes to human lung tumorigenesis . Oncogene doi:10.1038/onc.2013.239 ( 2013 ).
  • Reisman D , GlarosS , ThompsonEA . The SWI/SNF complex and cancer . Oncogene28 ( 14 ), 1653 – 1668 ( 2009 ).
  • Kurdistani SK . Histone modifications in cancer biology and prognosis . Prog. Drug Res.67 , 91 – 106 ( 2011 ).
  • Seligson DB , HorvathS , McbrianMAet al. Global levels of histone modifications predict prognosis in different cancers . Am.J. Pathol.174 ( 5 ), 1619 – 1628 ( 2009 ).
  • Reisman DN , SciarrottaJ , WangW , FunkhouserWK , WeissmanBE . Loss of BRG1/BRM in human lung cancer cell lines and primary lung cancers: correlation with poor prognosis . Cancer Res.63 ( 3 ), 560 – 566 ( 2003 ).
  • Fukuoka J , FujiiT , ShihJHet al. Chromatin remodeling factors and BRM/BRG1 expression as prognostic indicators in non-small cell lung cancer . Clin, Cancer Res.10 ( 13 ), 4314 – 4324 ( 2004 ).
  • Rodriguez-Paredes M , EstellerM . Cancer epigenetics reaches mainstream oncology . Nat. Med.17 ( 3 ), 330 – 339 ( 2011 ).
  • Shames DS , ElkinsK , WalterKet al. Loss of NAPRT1 expression by tumor-specific promoter methylation provides a novel predictive biomarker for NAMPT inhibitors . Clin. Cancer Res.19 ( 24 ) 6912 – 6923 ( 2013 ).
  • Fujii M , FujimotoN , HirakiAet al. Aberrant DNA methylation profile in pleural fluid for differential diagnosis of malignant pleural mesothelioma . Cancer Sci.103 ( 3 ), 510 – 514 ( 2012 ).
  • Schmidt B , LiebenbergV , DietrichDet al. SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer based on bronchial aspirates . BMC Cancer10 , 600 ( 2010 ).
  • Kneip C , SchmidtB , SeegebarthAet al. SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer in plasma . J. Thorac. Oncol.6 ( 10 ), 1632 – 1638 ( 2011 ).
  • Lokk K , VooderT , KoldeRet al. Methylation markers of early-stage non-small cell lung cancer . PloS ONE7 ( 6 ), e39813 ( 2012 ).
  • Lockwood WW , WilsonIM , CoeBPet al. Divergent genomic and epigenomic landscapes of lung cancer subtypes underscore the selection of different oncogenic pathways during tumor development . PloS ONE7 ( 5 ), e37775 ( 2012 ).
  • Selamat SA , ChungBS , GirardLet al. Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression . Genome Res.22 ( 7 ), 1197 – 1211 ( 2012 ).
  • De Fraipont F , LevalletG , CreveuilCet al. An apoptosis methylation prognostic signature for early lung cancer in the IFCT-0002 trial . Clin. Cancer Res.18 ( 10 ), 2976 – 2986 ( 2012 ).
  • Brock MV , HookerCM , Ota-MachidaEet al. DNA methylation markers and early recurrence in stage I lung cancer . N. Engl. J. Med.358 ( 11 ), 1118 – 1128 ( 2008 ).
  • Tessema M , YinglingCM , ThomasCLet al. SULF2 methylation is prognostic for lung cancer survival and increases sensitivity to topoisomerase-I inhibitors via induction of ISG15 . Oncogene31 ( 37 ), 4107 – 4116 ( 2012 ).
  • Cortes-Sempere M , DeMiguel MP , PerniaOet al. IGFBP-3 methylation-derived deficiency mediates the resistance to cisplatin through the activation of the IGFIR/Akt pathway in non-small cell lung cancer . Oncogene32 ( 10 ), 1274 – 1283 ( 2013 ).
  • Balgkouranidou I , LiloglouT , LianidouES . Lung cancer epigenetics: emerging biomarkers . Biomarkers Med.7 ( 1 ), 49 – 58 ( 2013 ).
  • Toyooka S , GazdarAF . Methylation profiling of lung cancer: a decade of progress . Mol. Cancer Ther.10 ( 11 ), 2020 ( 2011 ).
  • Zuo T , TyckoB , LiuTM , LinJJ , HuangTH . Methods in DNA methylation profiling . Epigenomics1 ( 2 ), 331 – 345 ( 2009 ).
  • Feinberg AP . Genome-scale approaches to the epigenetics of common human disease . Virchows Arch.456 ( 1 ), 13 – 21 ( 2010 ).
  • Bock C , TomazouEM , BrinkmanABet al. Quantitative comparison of genome-wide DNA methylation mapping technologies . Nat. Biotechnol.28 ( 10 ), 1106 – 1114 ( 2010 ).
  • Cokus SJ , FengS , ZhangXet al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning . Nature452 ( 7184 ), 215 – 219 ( 2008 ).
  • Lister R , EckerJR . Finding the fifth base: genome-wide sequencing of cytosine methylation . Genome Res.19 ( 6 ), 959 – 966 ( 2009 ).
  • Lister R , O’malleyRC , Tonti-FilippiniJet al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis . Cell133 ( 3 ), 523 – 536 ( 2008 ).
  • Lister R , PelizzolaM , DowenRHet al. Human DNA methylomes at base resolution show widespread epigenomic differences . Nature462 ( 7271 ), 315 – 322 ( 2009 ).
  • Sandoval J , HeynH , MoranSet al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome . Epigenetics6 ( 6 ), 692 – 702 ( 2011 ).
  • Touleimat N , TostJ . Complete pipeline for Infinium((R)) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation . Epigenomics4 ( 3 ), 325 – 341 ( 2012 ).
  • Hansen KD , TimpW , BravoHCet al. Increased methylation variation in epigenetic domains across cancer types . Nat. Genet.43 ( 8 ), 768 – 775 ( 2011 ).
  • Irizarry RA , Ladd-AcostaC , WenBet al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores . Nat. Genet.41 ( 2 ), 178 – 186 ( 2009 ).
  • Bock C . Analysing and interpreting DNA methylation data . Nat. Rev. Genet.13 ( 10 ), 705 – 719 ( 2012 ).
  • Ivanov M , KalsM , KacevskaM , MetspaluA , Ingelman-SundbergM , MilaniL . In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes . Nucleic Acids Res.41 ( 6 ), e72 ( 2013 ).
  • Smith ZD , GuH , BockC , GnirkeA , MeissnerA . High-throughput bisulfite sequencing in mammalian genomes . Methods48 ( 3 ), 226 – 232 ( 2009 ).
  • Meissner A , GnirkeA , BellGW , RamsahoyeB , LanderES , JaenischR . Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis . Nucleic Acids Res.33 ( 18 ), 5868 – 5877 ( 2005 ).
  • Boyle P , ClementK , GuHet al. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling . Genome Biol.13 ( 10 ), R92 ( 2012 ).
  • Ziller MJ , GuH , MullerFet al. Charting a dynamic DNA methylation landscape of the human genome . Nature500 ( 7463 ), 477 – 481 ( 2013 ).
  • Ostrow KL , HoqueMO , LoyoMet al. Molecular analysis of plasma DNA for the early detection of lung cancer by quantitative methylation-specific PCR . Clin. Cancer Res.16 ( 13 ), 3463 – 3472 ( 2010 ).
  • Migheli F , StoccoroA , CoppedeFet al. Comparison study of MS-HRM and pyrosequencing techniques for quantification of APC and CDKN2A gene methylation . PloS ONE8 ( 1 ), e52501 ( 2013 ).
  • Markopoulou S , NikolaidisG , LiloglouT . DNA methylation biomarkers in biological fluids for early detection of respiratory tract cancer . Clin. Chem. Lab. Med.50 ( 10 ), 1723 – 1731 ( 2012 ).
  • Begum S , BraitM , DasguptaSet al. An epigenetic marker panel for detection of lung cancer using cell-free serum DNA . Clin. Cancer Res.17 ( 13 ), 4494 – 4503 ( 2011 ).
  • Guzman L , DepixMS , SalinasAMet al. Analysis of aberrant methylation on promoter sequences of tumor suppressor genes and total DNA in sputum samples: a promising tool for early detection of COPD and lung cancer in smokers . Diagn. Pathol.7 , 87 ( 2012 ).
  • Leng S , DoK , YinglingCMet al. Defining a gene promoter methylation signature in sputum for lung cancer risk assessment . Clin. Cancer Res.18 ( 12 ), 3387 – 3395 ( 2012 ).
  • Li M , ChenWD , PapadopoulosNet al. Sensitive digital quantification of DNA methylation in clinical samples . Nat. Biotechnol.27 ( 9 ), 858 – 863 ( 2009 ).
  • Garcia-Gimenez JL , Sanchis-GomarF , LippiGet al. Epigenetic biomarkers: a new perspective in laboratory diagnostics . Clin. Chimica Acta413 ( 19-20 ), 1576 – 1582 ( 2012 ).
  • Hurteau GJ , CarlsonJA , SpivackSD , BrockGJ . Overexpression of the microRNA hsa-miR-200c leads to reduced expression of transcription factor 8 and increased expression of E-cadherin . Cancer Res.67 ( 17 ), 7972 – 7976 ( 2007 ).
  • Vrba L , GarbeJC , StampferMR , FutscherBW . Epigenetic regulation of normal human mammary cell type-specific miRNAs . Genome Res.21 ( 12 ), 2026 – 2037 ( 2011 ).
  • Doi A , ParkIH , WenBet al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts . Nature Genet.41 ( 12 ), 1350 – 1353 ( 2009 ).
  • Wu H , CaffoB , JaffeeHA , IrizarryRA , FeinbergAP . Redefining CpG islands using hidden Markov models . Biostatistics11 ( 3 ), 499 – 514 ( 2010 ).
  • Bediaga NG , DaviesMP , Acha-SagredoAet al. A microRNA-based prediction algorithm for diagnosis of non-small lung cell carcinoma in minimal biopsy material . Br. J. Cancer456 ( 1 ), 13 – 21 ( 2013 ).
  • Nikolaidis G , RajiOY , MarkopoulouSet al. DNA methylation biomarkers offer improved diagnostic efficiency in lung cancer . Cancer Res.72 ( 22 ), 5692 – 5701 ( 2012 ).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.