title: Expression of microRNAs in the NCI-60 cancer cell-lines.
abstract: The NCI-60 panel of 60 human cancer cell-lines of nine different tissues of origin has been extensively characterized in biological, molecular and pharmacological studies. Analyses of data from such studies have provided valuable information for understanding cellular processes and developing strategies for the diagnosis and treatment of cancer. Here, Affymetrix® GeneChip™ miRNA version 1 oligonucleotide microarrays were used to quantify 847 microRNAs to generate an expression dataset of 495 (58.4%) microRNAs that were identified as expressed in at least one cell-line of the NCI-60 panel. Accuracy of the microRNA measurements was partly confirmed by reverse transcription and polymerase chain reaction assays. Similar to that seen among the four existing NCI-60 microRNA datasets, the concordance of the new expression dataset with the other four was modest, with mean Pearson correlation coefficients of 0.37-0.54. In spite of this, comparable results with different datasets were noted in clustering of the cell-lines by their microRNA expression, differential expression of microRNAs by the lines' tissue of origin, and correlation of specific microRNAs with the doubling-time of cells or their radiation sensitivity. Mutation status of the cell-lines for the TP53, PTEN and BRAF but not CDKN2A or KRAS cancer-related genes was found to be associated with changes in expression of specific microRNAs. The microRNA dataset generated here should be valuable to those working in the field of microRNAs as well as in integromic studies of the NCI-60 panel.
authors.affiliation: Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Santosh K
authors.initials: SK
authors.lastname: Patnaik
authors.forename: Jesper
authors.initials: J
authors.lastname: Dahlgaard
authors.forename: Wiktor
authors.initials: W
authors.lastname: Mazin
authors.forename: Eric
authors.initials: E
authors.lastname: Kannisto
authors.forename: Thomas
authors.initials: T
authors.lastname: Jensen
authors.forename: Steen
authors.initials: S
authors.lastname: Knudsen
authors.forename: Sai
authors.initials: S
authors.lastname: Yendamuri
mesh_terms: D045744:Cell Line, Tumor; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000528:radiation effects; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D009857:Oncogenes; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger