{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Jigui Shan"],"study_type":["other"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-42962"],"description":["MicroRNAs are critical mediators of stem cell pluripotency, differentiation and malignancy.  Limited information exists regarding microRNA alterations that facilitate initiation and progression of human lung cancers.  In this study, array techniques were used to evaluate microRNA expression in normal human respiratory epithelia and lung cancer cells cultured in the presence or absence of cigarette smoke condensate (CSC).  Under relevant exposure conditions, CSC significantly repressed miR-487b in these cells.  Subsequent experiments demonstrated that miR-487b directly targets SUZ12, BMI1, Wnt5a, c-Myc and K-ras.  Repression of miR-487b correlated with over-expression of these targets in primary lung cancers, and coincided with DNA methylation, de-novo nucleosome occupancy, and decreased H2AZ and TCF1 levels within the miR-487b genomic locus.  Deoxyazacytidine de-repressed miR-487b, and attenuated CSC-mediated silencing of miR-487b.  TGF-?1 recapitulated CSC-mediated repression of miR-487b.  Constitutive expression of miR-487b abrogated Wnt signaling; inhibited in-vitro proliferation and invasion of lung cancer cells mediated by CSC or over-expression of miR-487b targets, and decreased growth and metastatic potential of lung cancer cells in-vivo.  Collectively, these findings indicate that miR-487b is a novel tumor suppressor microRNA silenced by epigenetic mechanisms during tobacco-induced pulmonary carcinogenesis, and suggest that DNA demethylating agents may be useful for activating miR-487b for lung cancer therapy. MicroRNA PCR array analysis.  Human RT2 miRNA PCR Arrays (MAH-3100E-12) were obtained from SA Biosciences.  Two hundred ng of isolated miRNA was used for reverse transcription and the entire first strand cDNA was diluted and distributed amongst the 384 wells of the super-array plate. The reactions were performed with RT² SYBR Green / ROX PCR Master Mix (SABiosciences).  Results were analyzed using software provided by the vendor (http://www.sabiosciences.com/pcr/arrayanalysis.php)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - All lung cancer lines were obtained from American Type Culture Collection (ATCC). NCI-SB-EsC2 (EsC2) was established in our lab; OE-33 was purchased from Sigma. All cancer lines were maintained in RPMI media supplemented with 10% FCS, 10 mM of glutamic acid, and 1% penicillin/streptomycin (normal media). Primary normal human small airway epithelial cells (SAEC) were obtained from Lonza, Inc., and cultured per vendor instructions. Immortalized human bronchial epithelial cells (HBEC) were generously provided by John D. Minna (U-T Southwestern, Dallas, TX), and cultured as described (64).","Sample Processing - Cigarette smoke condensates (CSC) derived from Kentucky Reference 3R4F research blend cigarettes (University of Kentucky) were prepared as described (64), and resuspended at a concentration of 10 mg tar/ml in DMSO as stock concentration. For smoke exposure experiments, cells were cultured in 10-cm dishes in appropriate normal media (NM) with DMSO or NM with CSC (0.02mg/ml). Medium was changed daily with the addition of fresh CSC or DMSO control.","Nucleic Acid Extraction - Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.","Labeling - PCR assays were performed using specific primers for mature miRNAs (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions.","Hybridization - n/a"],"figure_sub":["MIAME Score","Organization","Assays and Data","Processed Data","MAGE-TAB Files"],"pubmed_authors":["Jigui Shan","Sichuan Xi","Hong Xu","David Schrump"],"data_protocol":["Assay Data Transformation - ID_REF =  VALUE = normalized signal intensity","Image Adquisition - n/a","Feature Extraction - The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php Fold Change worksheet reports test/control (i.e., CSC treatment/ DMSO control) ratios."],"additional_accession":[]},"is_claimable":false,"name":"SABiosciences Human miRNA PCR array assay of normal respiratory epithelia and lung cancer cells with or without treatment of CSC","description":"MicroRNAs are critical mediators of stem cell pluripotency, differentiation and malignancy.  Limited information exists regarding microRNA alterations that facilitate initiation and progression of human lung cancers.  In this study, array techniques were used to evaluate microRNA expression in normal human respiratory epithelia and lung cancer cells cultured in the presence or absence of cigarette smoke condensate (CSC).  Under relevant exposure conditions, CSC significantly repressed miR-487b in these cells.  Subsequent experiments demonstrated that miR-487b directly targets SUZ12, BMI1, Wnt5a, c-Myc and K-ras.  Repression of miR-487b correlated with over-expression of these targets in primary lung cancers, and coincided with DNA methylation, de-novo nucleosome occupancy, and decreased H2AZ and TCF1 levels within the miR-487b genomic locus.  Deoxyazacytidine de-repressed miR-487b, and attenuated CSC-mediated silencing of miR-487b.  TGF-?1 recapitulated CSC-mediated repression of miR-487b.  Constitutive expression of miR-487b abrogated Wnt signaling; inhibited in-vitro proliferation and invasion of lung cancer cells mediated by CSC or over-expression of miR-487b targets, and decreased growth and metastatic potential of lung cancer cells in-vivo.  Collectively, these findings indicate that miR-487b is a novel tumor suppressor microRNA silenced by epigenetic mechanisms during tobacco-induced pulmonary carcinogenesis, and suggest that DNA demethylating agents may be useful for activating miR-487b for lung cancer therapy. MicroRNA PCR array analysis.  Human RT2 miRNA PCR Arrays (MAH-3100E-12) were obtained from SA Biosciences.  Two hundred ng of isolated miRNA was used for reverse transcription and the entire first strand cDNA was diluted and distributed amongst the 384 wells of the super-array plate. The reactions were performed with RT² SYBR Green / ROX PCR Master Mix (SABiosciences).  Results were analyzed using software provided by the vendor (http://www.sabiosciences.com/pcr/arrayanalysis.php).","dates":{"release":"2012-12-18T00:00:00Z","modification":"2023-09-01T12:42:02.101Z","creation":"2021-10-14T15:05:36Z"},"accession":"E-GEOD-42962","cross_references":{"GEO":["GSE42962"]}}