title: Genome-wide analysis of DNA methylation and their associations with long noncoding RNA/mRNA expression in non-small-cell lung cancer.
abstract: OBJECTIVE
  The goal of this study is to identify differentially methylated (DM) loci associated with long noncoding RNA (lncRNA)/mRNA expression in non-small-cell lung cancer (NSCLC).
  
  
  METHODS
  Microarrays were used to interrogate genome-wide methylation and expression of lncRNA/mRNA in NSCLC.
  
  
  RESULTS
  We identified 113,644 DM loci between tumors and adjacent tissues. Among them, 26,310 DM loci were associated with 1685 differentially expressed genes, and 839 genes had significant correlations between methylation and expression, of which 26 hypermethylated loci in transcription start site 200 were correlated with low gene expression. We validated the correlations between methylation and expression in five genes (CDO1, C2orf40, SCARF1, ZFP106 and IFFO1) using pyrosequencing and quantitative polymerase chain reaction. We also found significant correlations between lncRNAs and mRNAs, and validated four of the correlations with quantitative polymerase chain reaction.
  
  
  CONCLUSIONS
  Integrated analysis of genome-wide DNA methylation and lncRNA/mRNA expression allows us to identify new DM loci-correlated with gene expression in NSCLC.
authors.affiliation: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
authors.forename: Nannan
authors.initials: N
authors.lastname: Feng
authors.affiliation: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.|Tianjin Key Laboratory of Cancer Prevention & Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
authors.forename: Min
authors.initials: M
authors.lastname: Zheng
authors.affiliation: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Yu
authors.affiliation: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Lin
authors.affiliation: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
authors.forename: Rong-Na
authors.initials: RN
authors.lastname: Ma
authors.affiliation: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
authors.forename: Oumin
authors.initials: O
authors.lastname: Shi
authors.affiliation: Tianjin Key Laboratory of Cancer Prevention & Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China.
authors.forename: Xiangqian
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Tianjin Key Laboratory of Cancer Prevention & Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Gao
authors.affiliation: Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI 96813, USA.
authors.forename: Herbert
authors.initials: H
authors.lastname: Yu
authors.affiliation: Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI 96813, USA.
authors.forename: Lana
authors.initials: L
authors.lastname: Garmire
authors.affiliation: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
authors.forename: Biyun
authors.initials: B
authors.lastname: Qian
keywords: genome-wide methylation; long noncoding RNA; lung cancer; microarray expression