title: Genome-wide miRNA expression profiling identifies miR-9-3 and miR-193a as targets for DNA methylation in non-small cell lung cancers.
abstract: OBJECTIVE
  The major aim of this study was to investigate the role of DNA methylation (referred to as methylation) on miRNA silencing in non-small cell lung cancers (NSCLC).
  
  
  METHODS
  We conducted microarray expression analyses of 856 miRNAs in NSCLC A549 cells before and after treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (Aza-dC) and with a combination of Aza-dC and the histone deacetylase inhibitor trichostatin A. miRNA methylation was determined in 11 NSCLC cell lines and in primary tumors and corresponding nonmalignant lung tissue samples of 101 patients with stage I-III NSCLC.
  
  
  RESULTS
  By comparing microarray data of untreated and drug-treated A549 cells, we identified 33 miRNAs whose expression was upregulated after drug treatment and which are associated with a CpG island. Thirty (91%) of these miRNAs were found to be methylated in at least 1 of 11 NSCLC cell lines analyzed. Moreover, miR-9-3 and miR-193a were found to be tumor specifically methylated in patients with NSCLC. We observed a shorter disease-free survival of patients with miR-9-3 methylated lung squamous cell carcinoma (LSCC) than patients with miR-9-3 unmethylated LSCC by multivariate analysis [HR = 3.8; 95% confidence interval (CI), 1.3-11.2, P = 0.017] and a shorter overall survival of patients with miR-9-3 methylated LSCC than patients with miR-9-3 unmethylated LSCC by univariate analysis (P = 0.013).
  
  
  CONCLUSIONS
  Overall, our results suggest that methylation is an important mechanism for inactivation of certain miRNAs in NSCLCs and that miR-9-3 methylation may serve as a prognostic parameter in patients with LSCC.
authors.affiliation: Department of Medicine I, Medical University of Vienna, Vienna, Austria.
authors.forename: Gerwin
authors.initials: G
authors.lastname: Heller
authors.forename: Marlene
authors.initials: M
authors.lastname: Weinzierl
authors.forename: Christian
authors.initials: C
authors.lastname: Noll
authors.forename: Valerie
authors.initials: V
authors.lastname: Babinsky
authors.forename: Barbara
authors.initials: B
authors.lastname: Ziegler
authors.forename: Corinna
authors.initials: C
authors.lastname: Altenberger
authors.forename: Christoph
authors.initials: C
authors.lastname: Minichsdorfer
authors.forename: György
authors.initials: G
authors.lastname: Lang
authors.forename: Balazs
authors.initials: B
authors.lastname: Döme
authors.forename: Adelheid
authors.initials: A
authors.lastname: End-Pfützenreuter
authors.forename: Britt-Madeleine
authors.initials: BM
authors.lastname: Arns
authors.forename: Yuliya
authors.initials: Y
authors.lastname: Grin
authors.forename: Walter
authors.initials: W
authors.lastname: Klepetko
authors.forename: Christoph C
authors.initials: CC
authors.lastname: Zielinski
authors.forename: Sabine
authors.initials: S
authors.lastname: Zöchbauer-Müller
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics*; D045744:Cell Line, Tumor; D019175:DNA Methylation; D000077209:Decitabine; D005260:Female; D020869:Gene Expression Profiling; D020868:Gene Silencing; D006801:Humans; D006877:Hydroxamic Acids / Q000494:pharmacology; D008168:Lung / Q000378:metabolism; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D035683:MicroRNAs / Q000378:metabolism*; D008875:Middle Aged; D058990:Molecular Targeted Therapy; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D000970:Antineoplastic Agents; D006877:Hydroxamic Acids; C546818:MIRN193 microRNA, human; C541874:MIRN92 microRNA, human; D035683:MicroRNAs; C012589:trichostatin A; D000077209:Decitabine; D001374:Azacitidine