Comprehensive Epigenetic Analysis of the Signature Genes in Lung Adenocarcinoma

References

• Jemal A , BrayF , CenterMM , FerlayJ , WardE , FormanD . Global cancer statistics . CA Cancer J. Clin.61 ( 2 ), 69 – 90 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Molina JR , YangP , CassiviSD , SchildSE , AdjeiAA . Non-small-cell lung cancer: epidemiology, risk factors, treatment, and survivorship . Mayo Clin. Proc.83 ( 5 ), 584 – 594 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Tian Z , WenS , ZhangYet al. Identification of dysregulated long non-coding RNAs/microRNAs/mRNAs in TNM I stage lung adenocarcinoma . Oncotarget doi:10.18632/oncotarget.18512 ( 2017 ) ( Epub ahead of print ).
   Google Scholar
• Ricordel C , Labalette-TiercinM , LespagnolAet al. EFGR-mutant lung adenocarcinoma and Li–Fraumeni syndrome: report of two cases and review of the literature . Lung Cancer87 ( 1 ), 80 – 84 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Yano T , HaroA , ShikadaY , MaruyamaR , MaeharaY . Non-small-cell lung cancer in never smokers as a representative ‘non-smoking-associated lung cancer’: epidemiology and clinical features . Int. J. Clin. Oncol.16 ( 4 ), 287 – 293 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Du J , ZhangL . Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome . Oncol. Rep.34 ( 2 ), 585 – 594 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Suzuki A , MakinoshimaH , WakaguriHet al. Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines . Nucleic Acids Res.42 ( 22 ), 13557 – 13572 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Yang ZH , ZhengR , GaoY , ZhangQ , ZhangH . Abnormal gene expression and gene fusion in lung adenocarcinoma with high-throughput RNA sequencing . Cancer Gene Ther.21 ( 2 ), 74 – 82 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Seo JS , JuYS , LeeWCet al. The transcriptional landscape and mutational profile of lung adenocarcinoma . Genome Res.22 ( 11 ), 2109 – 2119 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Zhang S , ZhongB , ChenMet al. Epigenetic reprogramming reverses the malignant epigenotype of the MMP/TIMP axis genes in tumor cells . Int. J. Cancer134 ( 7 ), 1583 – 1594 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Valdmanis PN , Roy-ChaudhuriB , KimHKet al. Upregulation of the microRNA cluster at the Dlk1-Dio3 locus in lung adenocarcinoma . Oncogene34 ( 1 ), 94 – 103 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Johnson SM , GrosshansH , ShingaraJet al. RAS is regulated by the let-7 microRNA family . Cell120 ( 5 ), 635 – 647 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Heyn H , EstellerM . DNA methylation profiling in the clinic: applications and challenges . Nat. Rev. Genet.13 ( 10 ), 679 – 692 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Esteller M . Epigenetics in cancer . N. Engl. J. Med.358 ( 11 ), 1148 – 1159 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Esteller M . Epigenetic gene silencing in cancer: the DNA hypermethylome . Hum. Mol. Genet.16 ( R1 ), R50 – R59 ( 2007 ).
   PubMedGoogle Scholar
• Robertson KD . DNA methylation and human disease . Nat. Rev. Genet.6 ( 8 ), 597 – 610 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• 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 ).
   PubMed Web of Science ®Google Scholar
• Anders S , HuberW . Differential expression analysis for sequence count data . Genome Biol.11 ( 10 ), R106 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Benjamini Y , HochbergY . Controlling the false discovery rate: a practical and powerful approach to multiple testing . J. R Stat. Soc. Series B (Methodol.)57 ( 1 ), 289 – 300 ( 1995 ).
   Google Scholar
• Warden CD , LeeH , TompkinsJDet al. COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis . Nucleic Acids Res.41 ( 11 ), e117 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Smoot ME , OnoK , RuscheinskiJ , WangPL , IdekerT . Cytoscape 2.8: new features for data integration and network visualization . Bioinformatics27 ( 3 ), 431 – 432 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Young MD , WakefieldMJ , SmythGK , OshlackA . Gene ontology analysis for RNA-seq: accounting for selection bias . Genome Biol.11 ( 2 ), R14 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Kanehisa M , GotoS . KEGG: kyoto encyclopedia of genes and genomes . Nucleic Acids Res.28 ( 1 ), 27 – 30 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Bustin SA , BenesV , GarsonJAet al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments . Clin. Chem.55 ( 4 ), 611 – 622 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Robin X , TurckN , HainardAet al. pROC: an open-source package for R and S+ to analyze and compare ROC curves . BMC Bioinformatics12 , 77 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Saito M , ShiraishiK , KunitohH , TakenoshitaS , YokotaJ , KohnoT . Gene aberrations for precision medicine against lung adenocarcinoma . Cancer Sci.107 ( 6 ), 713 – 720 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Krasnov GS , DmitrievAA , MelnikovaNVet al. CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms . Nucleic Acids Res.44 ( 7 ), e62 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Tiger CF , FougerousseF , GrundstromG , VellingT , GullbergD . Alpha11beta1 integrin is a receptor for interstitial collagens involved in cell migration and collagen reorganization on mesenchymal nonmuscle cells . Dev. Biol.237 ( 1 ), 116 – 129 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Wang KK , LiuN , RadulovichNet al. Novel candidate tumor marker genes for lung adenocarcinoma . Oncogene21 ( 49 ), 7598 – 7604 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Chong IW , ChangMY , ChangHCet al. Great potential of a panel of multiple hMTH1, SPD, ITGA11 and COL11A1 markers for diagnosis of patients with non-small-cell lung cancer . Oncol. Rep.16 ( 5 ), 981 – 988 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Xu JB , BaoY , LiuX , LiuY , HuangS , WangJC . Defective expression of transforming growth factor beta type II receptor (TGFBR2) in the large cell variant of non-small-cell lung carcinoma . Lung Cancer58 ( 1 ), 36 – 43 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Dmitriev AA , KashubaVI , HaraldsonKet al. Genetic and epigenetic analysis of non-small-cell lung cancer with NotI-microarrays . Epigenetics7 ( 5 ), 502 – 513 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Qu H , ZhuM , TaoY , ZhaoY . Suppression of peripheral myelin protein 22 (PMP22) expression by miR29 inhibits the progression of lung cancer . Neoplasma62 ( 6 ), 881 – 886 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Iruela-Arispe ML , LuqueA , LeeN . Thrombospondin modules and angiogenesis . Int. J. Biochem. Cell Biol.36 ( 6 ), 1070 – 1078 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Lawler J . The functions of thrombospondin-1 and-2 . Curr. Opin. Cell Biol.12 ( 5 ), 634 – 640 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Chijiwa T , AbeY , InoueYet al. Cancerous, but not stromal, thrombospondin-2 contributes prognosis in pulmonary adenocarcinoma . Oncol. Rep.22 ( 2 ), 279 – 283 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Metodieva SN , NikolovaDN , ChernevaRV , DimovaIi , PetrovDB , TonchevaDI . Expression analysis of angiogenesis-related genes in Bulgarian patients with early-stage non-small-cell lung cancer . Tumori97 ( 1 ), 86 – 94 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Tessema M , YinglingCM , SniderAMet al. GATA2 is epigenetically repressed in human and mouse lung tumors and is not requisite for survival of KRAS mutant lung cancer . J. Thorac. Oncol.9 ( 6 ), 784 – 793 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Zhang ML , NieFQ , SunMet al. HOXA5 indicates poor prognosis and suppresses cell proliferation by regulating p21 expression in non-small-cell lung cancer . Tumour Biol.36 ( 5 ), 3521 – 3531 ( 2015 ).
   PubMedGoogle Scholar
• Kim DS , KimMJ , LeeJYet al. Epigenetic inactivation of Homeobox A5 gene in non-small-cell lung cancer and its relationship with clinicopathological features . Mol. Carcinog.48 ( 12 ), 1109 – 1115 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Huang T , LiJ , ZhangCet al. Distinguishing lung adenocarcinoma from lung squamous cell carcinoma by two hypomethylated and three hypermethylated genes: a meta-analysis . PLoS ONE11 ( 2 ), e0149088 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Yin D , JiaY , YuYet al. SOX17 methylation inhibits its antagonism of Wnt signaling pathway in lung cancer . Discov. Med.14 ( 74 ), 33 – 40 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Li W , HuangK , GuoH , CuiG . Meis1 regulates proliferation of non-small-cell lung cancer cells . J. Thorac. Dis.6 ( 6 ), 850 – 855 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Rauch TA , WangZ , WuX , KernstineKH , RiggsAD , PfeiferGP . DNA methylation biomarkers for lung cancer . Tumour Biol.33 ( 2 ), 287 – 296 ( 2012 ).
   PubMedGoogle Scholar
• Waddington CH . The epigenotype. 1942 . Int. J. Epidemiol.41 ( 1 ), 10 – 13 ( 2012 ).
   PubMed Web of Science ®Google Scholar